Variant report

Variant	rs1520203
Chromosome Location	chr3:191075012-191075013
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:191074353-191075159	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:191074387-191075088	Hela-S3	cervix:	n/a	n/a
3	SP1	chr3:191074317-191075305	HCT-116	colon:	n/a	n/a
4	TBP	chr3:191074536-191075069	Hela-S3	cervix:	n/a	n/a
5	FOS	chr3:191074461-191075193	HUVEC	blood vessel:	n/a	n/a
6	CEBPB	chr3:191074423-191075056	Hela-S3	cervix:	n/a	n/a
7	FOS	chr3:191074553-191075107	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD2	chr3:191074858-191075140	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr3:191074611-191075282	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr3:191074363-191075181	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr3:191074478-191075148	MCF10A-Er-Src	breast:	n/a	n/a
12	CBX3	chr3:191074379-191075227	HCT-116	colon:	n/a	n/a
13	STAT3	chr3:191074513-191075038	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:191074168-191075053	MCF10A-Er-Src	breast:	n/a	n/a
15	WRNIP1	chr3:191074849-191075145	GM12878	blood:	n/a	n/a
16	MYC	chr3:191074394-191075083	MCF10A-Er-Src	breast:	n/a	n/a
17	FOSL1	chr3:191074294-191075265	HCT-116	colon:	n/a	n/a
18	FOS	chr3:191074494-191075078	MCF10A-Er-Src	breast:	n/a	n/a
19	RFX5	chr3:191074452-191075216	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:191073947-191075439	PFSK-1	brain:	n/a	n/a
21	RCOR1	chr3:191074374-191075226	Hela-S3	cervix:	n/a	n/a
22	STAT3	chr3:191074750-191075169	MCF10A-Er-Src	breast:	n/a	n/a
23	USF2	chr3:191074849-191075049	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr3:191074752-191075166	MCF10A-Er-Src	breast:	n/a	n/a
25	TFAP2C	chr3:191074749-191075231	Hela-S3	cervix:	n/a	n/a
26	E2F4	chr3:191074719-191075036	MCF10A-Er-Src	breast:	n/a	n/a
27	GTF2F1	chr3:191074455-191075207	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr3:191074432-191075090	Hela-S3	cervix:	n/a	chr3:191074621-191074634
29	SMC3	chr3:191074466-191075071	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:191074841-191075066	HUVEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:191049298..191052407-chr3:191074621..191077632,4	K562	blood:
2	chr3:191059352..191062066-chr3:191073918..191075676,3	K562	blood:
3	chr3:191059352..191066044-chr3:191070268..191075568,9	K562	blood:
4	chr3:191049478..191053328-chr3:191074760..191077632,3	K562	blood:

No data

Variant related genes	Relation type
CCDC50	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11542549	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1435062	0.90[ASN][1000 genomes]
rs1473869	0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1520202	0.90[ASN][1000 genomes]
rs1609926	0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs16822378	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs16822382	0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs16848980	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs16866487	0.93[ASN][1000 genomes]
rs16866504	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs16866505	0.92[ASN][1000 genomes]
rs17753967	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17810246	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17810282	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17838893	0.93[ASN][1000 genomes]
rs2056333	0.93[ASN][1000 genomes]
rs2364379	0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28715898	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796219	0.90[ASN][1000 genomes]
rs3959143	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4677631	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677632	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677725	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677726	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677727	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56174842	0.93[ASN][1000 genomes]
rs57211729	0.93[ASN][1000 genomes]
rs58141749	0.88[ASN][1000 genomes]
rs58645265	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59709586	0.84[ASN][1000 genomes]
rs61250936	0.82[ASN][1000 genomes]
rs6444541	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73185209	0.96[ASN][1000 genomes]
rs73185210	0.98[ASN][1000 genomes]
rs73185213	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73185226	0.92[ASN][1000 genomes]
rs73185228	0.90[ASN][1000 genomes]
rs73185240	0.88[ASN][1000 genomes]
rs73185255	0.88[ASN][1000 genomes]
rs73185263	0.87[ASN][1000 genomes]
rs73185284	0.83[ASN][1000 genomes]
rs73185287	0.83[ASN][1000 genomes]
rs73185288	0.81[ASN][1000 genomes]
rs73201627	0.90[ASN][1000 genomes]
rs73201628	0.90[ASN][1000 genomes]
rs73201630	0.90[ASN][1000 genomes]
rs73201631	0.90[ASN][1000 genomes]
rs7637196	0.81[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642387	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648886	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9290986	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823680	0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824437	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839751	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9843934	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853569	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9863255	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876944	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv508266	chr3:191064212-191083637	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1808657	chr3:191064330-191081793	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv878106	chr3:191064528-191081344	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1823184	chr3:191064803-191082303	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1848120	chr3:191064803-191082303	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv592852	chr3:191073228-191093310	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv592853	chr3:191073228-191094985	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1520203	ADA	trans	cerebellum	SCAN
rs1520203	PPP1R2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191062000-191075600	Weak transcription	K562	blood
2	chr3:191062200-191075400	Weak transcription	Fetal Brain Female	brain
3	chr3:191063000-191076600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:191068600-191076600	Weak transcription	Fetal Kidney	kidney
5	chr3:191068800-191075400	Enhancers	Colon Smooth Muscle	Colon
6	chr3:191068800-191078800	Weak transcription	Fetal Brain Male	brain
7	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:191071000-191076000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:191071200-191076800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:191071200-191078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:191071200-191078800	Weak transcription	Lung	lung
13	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
14	chr3:191071400-191075800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:191071400-191078400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:191071400-191078800	Weak transcription	Gastric	stomach
17	chr3:191071400-191078800	Weak transcription	Pancreas	Pancrea
18	chr3:191071400-191078800	Weak transcription	Spleen	Spleen
19	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
20	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:191072200-191075600	Weak transcription	Fetal Intestine Large	intestine
23	chr3:191072400-191076400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:191072600-191075800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:191072800-191076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:191073200-191075200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:191073200-191075200	Enhancers	Left Ventricle	heart
29	chr3:191073200-191075200	Enhancers	Psoas Muscle	Psoas
30	chr3:191073200-191075200	Enhancers	Rectal Smooth Muscle	rectum
31	chr3:191073200-191075200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:191073200-191075400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:191073200-191075400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:191073200-191075400	Enhancers	Adipose Nuclei	Adipose
35	chr3:191073200-191077600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:191073200-191078000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:191073400-191075400	Enhancers	HSMMtube	muscle
38	chr3:191073400-191075400	Enhancers	Osteobl	bone
39	chr3:191073400-191075600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:191073400-191077600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:191073400-191077800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:191073400-191079200	Weak transcription	Fetal Thymus	thymus
43	chr3:191073600-191075400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:191073600-191075400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:191073600-191077400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr3:191073600-191077600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:191073600-191083000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:191073800-191075200	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr3:191073800-191075200	Enhancers	Ovary	ovary

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