Variant report

Variant	rs2277814
Chromosome Location	chr21:47409503-47409504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47401680..47403965-chr21:47408741..47410479,2	K562	blood:
2	chr21:47405747..47408135-chr21:47408185..47410527,3	K562	blood:
3	chr21:47407254..47409991-chr21:47416573..47418228,3	K562	blood:
4	chr21:47407254..47409991-chr21:47416573..47418228,2	K562	blood:
5	chr21:47405747..47408135-chr21:47408185..47410437,2	K562	blood:

Variant related genes	Relation type
ENSG00000142156	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13051496	0.80[ASN][1000 genomes]
rs2015400	0.80[CEU][hapmap]
rs2330328	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs2742071	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2839008	0.80[CEU][hapmap]
rs2839023	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs2839024	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs2839078	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3746993	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4819160	0.86[CEU][hapmap]
rs7278258	0.82[CHB][hapmap]
rs741954	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs760439	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9974290	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9975272	1.00[CHD][hapmap]
rs9975402	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9977276	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs9984438	0.80[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:36 , 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	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
25	nsv587931	chr21:47393268-47412660	Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
26	esv1802000	chr21:47394780-47476081	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
27	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer 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
28	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
29	nsv587932	chr21:47398411-47418311	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
30	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
31	nsv587933	chr21:47401193-47412703	Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
32	esv1824109	chr21:47401282-47431018	Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
33	nsv587934	chr21:47406601-47423389	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
34	esv1849213	chr21:47406836-47455584	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
35	nsv459310	chr21:47409503-47488387	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
36	nsv587935	chr21:47409503-47488387	Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2277814	PCBP3	cis	cerebellum	SCAN
rs2277814	FTCD	cis	cerebellum	SCAN
rs2277814	COL6A1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47403200-47414600	Weak transcription	Brain Substantia Nigra	brain
2	chr21:47403200-47415200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:47403200-47424600	Weak transcription	Small Intestine	intestine
4	chr21:47403200-47425000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr21:47403600-47409600	Weak transcription	Fetal Thymus	thymus
6	chr21:47403600-47414800	Strong transcription	Fetal Intestine Small	intestine
7	chr21:47404000-47424200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr21:47404000-47424600	Strong transcription	Aorta	Aorta
9	chr21:47404200-47414400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:47404200-47425200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:47404200-47425200	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr21:47404400-47409600	Weak transcription	Right Atrium	heart
13	chr21:47404400-47414600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:47404400-47419200	Strong transcription	Left Ventricle	heart
15	chr21:47405000-47414600	Weak transcription	Fetal Kidney	kidney
16	chr21:47405000-47417400	Weak transcription	Stomach Mucosa	stomach
17	chr21:47405000-47419400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr21:47405000-47423800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr21:47405000-47425400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr21:47405200-47425400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr21:47405200-47425400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:47405200-47425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr21:47405400-47423800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:47405400-47424800	Strong transcription	Fetal Brain Female	brain
25	chr21:47405400-47425200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr21:47405600-47413200	Strong transcription	Osteobl	bone
27	chr21:47405600-47419800	Strong transcription	Fetal Stomach	stomach
28	chr21:47405600-47423000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr21:47405800-47414400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:47406200-47412400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:47406400-47411600	Strong transcription	Adipose Nuclei	Adipose
32	chr21:47406400-47421400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr21:47406600-47425400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr21:47406800-47410400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr21:47407000-47411600	Weak transcription	Brain Hippocampus Middle	brain
36	chr21:47407000-47414400	Strong transcription	Fetal Intestine Large	intestine
37	chr21:47407400-47410200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:47407400-47410600	Weak transcription	Brain Anterior Caudate	brain
39	chr21:47407400-47411800	Weak transcription	Pancreas	Pancrea
40	chr21:47407400-47413800	Weak transcription	HSMM	muscle
41	chr21:47407600-47409600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:47407600-47409600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr21:47407600-47409600	Weak transcription	Liver	Liver
44	chr21:47407600-47409600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr21:47407600-47409800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr21:47407600-47409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr21:47407600-47410000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr21:47407600-47410600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr21:47407600-47410600	Weak transcription	NH-A	brain
50	chr21:47407600-47414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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