Variant report

Variant	rs7657711
Chromosome Location	chr4:57264426-57264427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10031012	0.82[EUR][1000 genomes]
rs10031550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10034154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11133438	0.80[EUR][1000 genomes]
rs11133439	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11724302	0.80[EUR][1000 genomes]
rs11733474	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12331363	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12331412	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13114104	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133016	0.89[EUR][1000 genomes]
rs13141793	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13147824	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1401912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474178	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1976815	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1996650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030365	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2139512	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28559894	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2899063	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796547	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3822003	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4167	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4865087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865100	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865101	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57503982	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59615456	0.81[EUR][1000 genomes]
rs62310633	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554349	0.89[EUR][1000 genomes]
rs6554352	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554355	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6826795	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841016	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6841053	0.83[ASN][1000 genomes]
rs6856845	0.81[EUR][1000 genomes]
rs7661712	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7683781	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7692385	0.88[EUR][1000 genomes]
rs7693683	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9312674	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9684298	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9997639	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7657711	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs7657711	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57271600	Weak transcription	Ovary	ovary
5	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
6	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
13	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
14	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:57255000-57266200	Weak transcription	NH-A	brain
20	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:57255000-57266600	Weak transcription	HSMM	muscle
24	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
29	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:57255200-57266800	Weak transcription	Fetal Kidney	kidney
31	chr4:57255200-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:57255200-57267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:57255200-57267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:57255200-57271600	Weak transcription	NHEK	skin
35	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:57255200-57275600	Weak transcription	NHLF	lung
37	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
41	chr4:57255400-57266000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:57255400-57266200	Weak transcription	Primary T cells from cord blood	blood
43	chr4:57255400-57266400	Weak transcription	HMEC	breast
44	chr4:57255400-57266800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:57255400-57272400	Weak transcription	Fetal Brain Male	brain
46	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:57255600-57266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:57255600-57272000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
50	chr4:57255800-57266400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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