Variant report

Variant	rs3770120
Chromosome Location	chr2:182352469-182352470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10930969	1.00[LWK][hapmap]
rs12479308	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs155091	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs155109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155110	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155111	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17224524	0.87[ASN][1000 genomes]
rs17224699	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17225354	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs17225382	0.84[ASN][1000 genomes]
rs17290351	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs17290693	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs2305588	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.87[ASN][1000 genomes]
rs2305589	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2305590	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3755021	1.00[CHB][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs3770124	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3770136	1.00[LWK][hapmap]
rs3770138	0.92[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv834476	chr2:182179249-182360259	Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770120	ZNF502	trans	cerebellum	SCAN
rs3770120	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182324400-182410400	Weak transcription	NHLF	lung
2	chr2:182324600-182360400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:182330000-182390200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:182331400-182363400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:182331400-182382200	Weak transcription	HMEC	breast
6	chr2:182332200-182353000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:182334600-182381400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:182335000-182366800	Weak transcription	Fetal Stomach	stomach
9	chr2:182335000-182405800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:182335200-182356200	Weak transcription	Gastric	stomach
11	chr2:182336800-182382800	Weak transcription	Small Intestine	intestine
12	chr2:182337000-182354000	Strong transcription	Primary B cells from cord blood	blood
13	chr2:182338200-182363400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:182338200-182378400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:182338200-182383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:182338200-182399400	Weak transcription	Colonic Mucosa	Colon
17	chr2:182338200-182406800	Strong transcription	Fetal Thymus	thymus
18	chr2:182338200-182406800	Weak transcription	Spleen	Spleen
19	chr2:182338400-182382200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:182338600-182354000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:182338600-182405600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:182339000-182381000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:182339200-182380600	Strong transcription	Dnd41	blood
24	chr2:182339400-182405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:182339800-182355200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:182340000-182354600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:182341800-182363400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:182344400-182352800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:182344400-182362000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:182344400-182367200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:182344600-182354600	Strong transcription	Primary T cells from cord blood	blood
32	chr2:182344600-182354600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:182345400-182353800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:182346000-182352600	Strong transcription	Thymus	Thymus
35	chr2:182346000-182356000	Strong transcription	HSMMtube	muscle
36	chr2:182346000-182378600	Weak transcription	Lung	lung
37	chr2:182346800-182361400	Weak transcription	Fetal Intestine Small	intestine
38	chr2:182347000-182353000	Strong transcription	GM12878-XiMat	blood
39	chr2:182347200-182399800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:182347400-182363400	Weak transcription	HSMM	muscle
41	chr2:182348200-182377400	Weak transcription	NH-A	brain
42	chr2:182348600-182359400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:182348800-182353200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:182349000-182360400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:182349400-182356200	Weak transcription	Liver	Liver
46	chr2:182349600-182365000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:182349600-182405800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:182349800-182355800	Weak transcription	Left Ventricle	heart
49	chr2:182350400-182353000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:182350400-182384600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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