Variant report

Variant	rs4588278
Chromosome Location	chr21:47392731-47392732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47391035..47393326-chr21:47704879..47707195,2	MCF-7	breast:
2	chr21:47389572..47393249-chr21:47393676..47397258,4	K562	blood:
3	chr21:47387372..47388982-chr21:47392168..47393871,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL6A1-1	chr21:47392727-47393090	XLOC_013986

Variant related genes	Relation type
ENSG00000160294	Chromatin interaction
ENSG00000182362	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2065336	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2150456	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2507743	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4819175	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8127526	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:40 , 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	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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
38	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
39	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
40	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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47390200-47393400	Enhancers	Fetal Lung	lung
2	chr21:47390200-47393800	Enhancers	Fetal Heart	heart
3	chr21:47390400-47392800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47390400-47392800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr21:47390400-47392800	Enhancers	HSMM	muscle
6	chr21:47390400-47393600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr21:47390600-47395400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr21:47390800-47392800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr21:47390800-47392800	Enhancers	Brain Cingulate Gyrus	brain
10	chr21:47390800-47392800	Enhancers	HSMMtube	muscle
11	chr21:47391000-47392800	Weak transcription	Liver	Liver
12	chr21:47391000-47392800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr21:47391000-47393600	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr21:47391000-47394600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr21:47391200-47393000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
16	chr21:47391200-47393000	Enhancers	NH-A	brain
17	chr21:47391200-47393400	Weak transcription	Fetal Kidney	kidney
18	chr21:47391200-47394200	Enhancers	Spleen	Spleen
19	chr21:47391400-47392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:47391400-47392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:47391400-47393000	Weak transcription	Brain Angular Gyrus	brain
22	chr21:47391600-47392800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr21:47391600-47393200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr21:47392000-47392800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:47392000-47392800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr21:47392000-47392800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr21:47392000-47392800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr21:47392000-47392800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
29	chr21:47392000-47392800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr21:47392000-47392800	Flanking Active TSS	NHDF-Ad	bronchial
31	chr21:47392000-47393000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
32	chr21:47392000-47393000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr21:47392000-47393000	Enhancers	Brain Substantia Nigra	brain
34	chr21:47392000-47393200	Bivalent Enhancer	Placenta	Placenta
35	chr21:47392000-47395200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr21:47392000-47395200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr21:47392200-47392800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr21:47392200-47392800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
39	chr21:47392200-47392800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr21:47392200-47393000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:47392200-47393000	Bivalent Enhancer	Esophagus	oesophagus
42	chr21:47392200-47393000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr21:47392200-47393200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr21:47392200-47393400	Enhancers	Primary B cells from cord blood	blood
45	chr21:47392200-47393400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr21:47392200-47393600	Flanking Active TSS	NHLF	lung
47	chr21:47392200-47394800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr21:47392200-47395200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr21:47392400-47392800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr21:47392400-47392800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links