Variant report

Variant	rs11701176
Chromosome Location	chr21:47392150-47392151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47391035..47393326-chr21:47704879..47707195,2	MCF-7	breast:
2	chr21:47389572..47393249-chr21:47393676..47397258,4	K562	blood:

Variant related genes	Relation type
ENSG00000182362	Chromatin interaction
ENSG00000160294	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1005467	0.80[ASN][1000 genomes]
rs13313848	0.91[ASN][1000 genomes]
rs2839073	0.92[ASN][1000 genomes]
rs2839075	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs34241237	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs364984	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804037	0.94[ASN][1000 genomes]
rs3827270	0.94[ASN][1000 genomes]
rs71324472	0.96[ASN][1000 genomes]
rs7278906	0.92[ASN][1000 genomes]
rs7278998	0.92[ASN][1000 genomes]
rs7279116	0.97[ASN][1000 genomes]
rs9976472	0.92[ASN][1000 genomes]
rs9978646	0.91[ASN][1000 genomes]
rs9984383	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:42 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
11	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
12	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
14	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
15	nsv914085	chr21:47342116-47433055	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
16	esv1848879	chr21:47343462-47455584	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
17	nsv914086	chr21:47352625-47445184	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
18	nsv914087	chr21:47352625-47453954	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
19	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
20	nsv914088	chr21:47358915-47419012	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
21	nsv914089	chr21:47383056-47453954	ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
22	nsv914090	chr21:47383056-47465205	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
23	nsv914091	chr21:47383056-47483799	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
24	nsv587881	chr21:47388151-47392150	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
25	nsv587882	chr21:47388151-47393268	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
26	nsv587883	chr21:47388151-47398411	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
27	nsv587887	chr21:47388253-47398411	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
28	nsv587891	chr21:47388355-47393268	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
29	nsv587896	chr21:47388406-47393268	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
30	nsv587897	chr21:47388406-47398411	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
31	nsv587902	chr21:47388460-47393268	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
32	nsv587903	chr21:47388460-47398411	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
33	nsv587907	chr21:47388560-47393268	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
34	nsv587914	chr21:47388611-47393268	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
35	nsv587918	chr21:47388714-47393268	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
36	nsv587922	chr21:47388875-47398411	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
37	nsv587925	chr21:47389083-47393268	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
38	nsv587926	chr21:47389144-47392150	Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
39	nsv587927	chr21:47389144-47393268	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
40	nsv587928	chr21:47389144-47398411	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
41	nsv587929	chr21:47389258-47398411	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
42	nsv587930	chr21:47389258-47423389	Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11701176	TFF1	cis	cerebellum	SCAN
rs11701176	FTCD	cis	cerebellum	SCAN
rs11701176	CHCHD6	trans	lymphoblastoid	seeQTL
rs11701176	COL6A1	cis	Artery Tibial	GTEx
rs11701176	COL6A1	cis	Artery Aorta	GTEx
rs11701176	COL6A1	cis	parietal	SCAN
rs11701176	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47390000-47392400	Enhancers	Fetal Muscle Leg	muscle
2	chr21:47390200-47392200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr21:47390200-47393400	Enhancers	Fetal Lung	lung
4	chr21:47390200-47393800	Enhancers	Fetal Heart	heart
5	chr21:47390400-47392200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr21:47390400-47392400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:47390400-47392600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr21:47390400-47392600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr21:47390400-47392600	Enhancers	Left Ventricle	heart
10	chr21:47390400-47392600	Enhancers	Ovary	ovary
11	chr21:47390400-47392800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:47390400-47392800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr21:47390400-47392800	Enhancers	HSMM	muscle
14	chr21:47390400-47393600	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr21:47390600-47392200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr21:47390600-47392200	Enhancers	NHLF	lung
17	chr21:47390600-47392400	Enhancers	Brain Germinal Matrix	brain
18	chr21:47390600-47395400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:47390800-47392400	Weak transcription	Pancreas	Pancrea
20	chr21:47390800-47392600	Bivalent Enhancer	Fetal Stomach	stomach
21	chr21:47390800-47392800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr21:47390800-47392800	Enhancers	Brain Cingulate Gyrus	brain
23	chr21:47390800-47392800	Enhancers	HSMMtube	muscle
24	chr21:47391000-47392200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr21:47391000-47392200	Weak transcription	Fetal Brain Female	brain
26	chr21:47391000-47392400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr21:47391000-47392600	Bivalent Enhancer	Colonic Mucosa	Colon
28	chr21:47391000-47392800	Weak transcription	Liver	Liver
29	chr21:47391000-47392800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
30	chr21:47391000-47393600	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr21:47391000-47394600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:47391200-47392400	Enhancers	Osteobl	bone
33	chr21:47391200-47393000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
34	chr21:47391200-47393000	Enhancers	NH-A	brain
35	chr21:47391200-47393400	Weak transcription	Fetal Kidney	kidney
36	chr21:47391200-47394200	Enhancers	Spleen	Spleen
37	chr21:47391400-47392400	Weak transcription	Fetal Brain Male	brain
38	chr21:47391400-47392400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr21:47391400-47392400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
40	chr21:47391400-47392600	Weak transcription	Lung	lung
41	chr21:47391400-47392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr21:47391400-47392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr21:47391400-47393000	Weak transcription	Brain Angular Gyrus	brain
44	chr21:47391600-47392800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr21:47391600-47393200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr21:47392000-47392200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
47	chr21:47392000-47392200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr21:47392000-47392200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr21:47392000-47392200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:47392000-47392200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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