Variant report

Variant	rs3775657
Chromosome Location	chr4:143051680-143051681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10003401	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10003713	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10006183	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10006284	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10006285	0.90[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10013734	1.00[GIH][hapmap]
rs10018345	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10029467	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10030014	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10032149	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10032328	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10032526	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap]
rs10519618	0.80[CEU][hapmap]
rs10519631	1.00[GIH][hapmap]
rs10519633	1.00[GIH][hapmap]
rs10519638	0.91[GIH][hapmap]
rs12330961	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12331260	0.83[ASN][1000 genomes]
rs12498546	0.94[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs12501475	0.81[JPT][hapmap]
rs12502469	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12641407	0.82[ASN][1000 genomes]
rs12642756	0.80[ASN][1000 genomes]
rs1390993	1.00[GIH][hapmap]
rs17015544	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs17015559	0.83[ASN][1000 genomes]
rs17015594	1.00[GIH][hapmap]
rs17654944	1.00[GIH][hapmap]
rs2270657	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs2270659	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2276942	0.90[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs2627828	1.00[GIH][hapmap]
rs2627829	1.00[GIH][hapmap]
rs28373344	0.83[ASN][1000 genomes]
rs3756117	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs3775630	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap]
rs3775639	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3775640	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs3775641	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs3775642	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3775643	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3775644	0.84[ASN][1000 genomes]
rs3775647	0.89[ASN][1000 genomes]
rs3775648	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3775649	0.89[ASN][1000 genomes]
rs3775650	0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3775651	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs3775652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3775653	0.84[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775654	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775655	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3775656	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775658	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4501295	1.00[GIH][hapmap]
rs4956435	1.00[GIH][hapmap]
rs55679069	0.83[ASN][1000 genomes]
rs55728718	0.84[ASN][1000 genomes]
rs55784399	0.84[ASN][1000 genomes]
rs56024852	0.84[ASN][1000 genomes]
rs56156331	0.84[ASN][1000 genomes]
rs6827500	0.80[ASN][1000 genomes]
rs6842783	0.82[CHB][hapmap];0.91[GIH][hapmap]
rs6845623	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs6848191	0.80[ASN][1000 genomes]
rs6848385	0.80[ASN][1000 genomes]
rs6850756	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs7697702	1.00[GIH][hapmap]
rs9308148	0.92[GIH][hapmap]
rs9985602	0.82[ASN][1000 genomes]
rs9986085	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs9995208	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs9998887	0.80[ASN][1000 genomes]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3775657	FAM92A1	trans	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:143025400-143066800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:143030000-143057000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:143031000-143064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:143034000-143061600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:143039200-143059000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:143042200-143060200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:143043400-143089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:143043600-143056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:143043800-143054000	Weak transcription	Psoas Muscle	Psoas
12	chr4:143045800-143057200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:143046400-143052200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:143046400-143054600	Weak transcription	HSMM	muscle
15	chr4:143046800-143057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:143049400-143051800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:143049400-143052200	Enhancers	Fetal Heart	heart
18	chr4:143049600-143052600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:143049600-143057200	Weak transcription	Lung	lung
20	chr4:143049800-143051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:143049800-143052000	Enhancers	Colon Smooth Muscle	Colon
22	chr4:143049800-143052400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr4:143049800-143052400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:143049800-143053000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:143049800-143055600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:143049800-143114400	Weak transcription	Right Ventricle	heart
27	chr4:143050000-143051800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:143050000-143052400	Enhancers	Stomach Smooth Muscle	stomach
29	chr4:143050000-143056600	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:143050000-143079600	Weak transcription	NHDF-Ad	bronchial
31	chr4:143050200-143052400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr4:143050200-143056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:143050200-143061000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:143050400-143053400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:143050400-143055000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr4:143050400-143056600	Weak transcription	HSMMtube	muscle
37	chr4:143050400-143062400	Weak transcription	Fetal Stomach	stomach
38	chr4:143050400-143063600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:143050600-143059800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:143050800-143056200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:143050800-143056200	Weak transcription	Dnd41	blood
42	chr4:143051000-143052400	Enhancers	Fetal Intestine Small	intestine
43	chr4:143051000-143052600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr4:143051200-143052000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:143051200-143052000	Genic enhancers	HMEC	breast
46	chr4:143051200-143052400	Enhancers	Fetal Intestine Large	intestine
47	chr4:143051200-143052400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr4:143051200-143052600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr4:143051200-143052600	Enhancers	A549	lung
50	chr4:143051400-143051800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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