Variant report

Variant	rs3774936
Chromosome Location	chr4:103434137-103434138
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103421642..103424651-chr4:103432017..103435020,7	MCF-7	breast:
2	chr4:103420745..103423144-chr4:103433405..103436115,3	MCF-7	breast:
3	chr4:103427680..103429888-chr4:103432571..103434498,2	MCF-7	breast:
4	chr4:103428188..103431133-chr4:103431767..103434518,2	MCF-7	breast:
5	chr4:103432462..103434714-chr4:103437509..103439750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11723120	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12509517	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1585213	1.00[JPT][hapmap]
rs1585215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1599961	1.00[JPT][hapmap]
rs17032705	1.00[JPT][hapmap]
rs170731	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230493	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230500	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230504	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230505	1.00[JPT][hapmap]
rs230509	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230515	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs230516	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs230519	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230520	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230526	1.00[JPT][hapmap]
rs230528	1.00[JPT][hapmap]
rs230529	1.00[JPT][hapmap]
rs230531	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230532	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230533	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230534	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230535	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs230540	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs230541	0.91[JPT][hapmap]
rs230542	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3755867	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774963	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3774964	0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	1.00[JPT][hapmap]
rs4648055	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4648058	0.91[JPT][hapmap]
rs4648068	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4648133	0.88[CEU][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.83[CEU][hapmap]
rs4699030	0.91[JPT][hapmap]
rs747559	1.00[JPT][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3774936	RGS20	trans	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103423800-103439800	Weak transcription	Ovary	ovary
2	chr4:103423800-103439800	Weak transcription	Pancreas	Pancrea
3	chr4:103423800-103439800	Weak transcription	Spleen	Spleen
4	chr4:103423800-103445800	Weak transcription	Lung	lung
5	chr4:103424000-103446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:103424800-103442400	Weak transcription	HSMM	muscle
7	chr4:103425200-103439800	Weak transcription	Right Ventricle	heart
8	chr4:103425200-103456400	Weak transcription	Osteobl	bone
9	chr4:103425600-103437200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:103425600-103448400	Weak transcription	Fetal Thymus	thymus
11	chr4:103426000-103435000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:103426000-103435600	Weak transcription	Brain Angular Gyrus	brain
13	chr4:103426000-103436000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:103426000-103439000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:103426000-103439200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:103426000-103444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:103426000-103452600	Weak transcription	NH-A	brain
18	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
19	chr4:103426200-103436600	Weak transcription	Dnd41	blood
20	chr4:103426200-103438800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:103426200-103439000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:103426200-103439600	Weak transcription	Stomach Mucosa	stomach
23	chr4:103426200-103445800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:103426400-103435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:103426400-103435400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:103426400-103439800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:103426400-103442800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:103426400-103442800	Weak transcription	NHEK	skin
29	chr4:103426400-103450000	Weak transcription	HMEC	breast
30	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
31	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:103427000-103439200	Weak transcription	Liver	Liver
33	chr4:103427600-103435600	Weak transcription	Fetal Lung	lung
34	chr4:103427800-103437200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:103428000-103442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
37	chr4:103429200-103446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:103431200-103434400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:103431200-103435400	Weak transcription	Left Ventricle	heart
40	chr4:103431400-103435400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:103431400-103435400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:103431400-103436000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:103431400-103438200	Weak transcription	Psoas Muscle	Psoas
44	chr4:103431400-103439000	Weak transcription	Small Intestine	intestine
45	chr4:103431400-103439200	Weak transcription	Adipose Nuclei	Adipose
46	chr4:103431400-103439800	Weak transcription	Gastric	stomach
47	chr4:103431600-103435400	Weak transcription	Primary T cells from cord blood	blood
48	chr4:103431800-103435600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:103431800-103447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:103432000-103437600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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