Variant report

Variant	rs10249366
Chromosome Location	chr7:97901860-97901861
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97900433..97904239-chr7:97908509..97910838,3	K562	blood:
2	chr7:97895252..97897059-chr7:97901681..97903186,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1076272	0.83[CEU][hapmap]
rs10953247	0.84[EUR][1000 genomes]
rs10953256	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs10953257	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs1132971	0.82[CHB][hapmap]
rs11761574	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11771397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11771953	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772438	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773779	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11984183	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533016	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12539676	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12669622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12704981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12704983	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs12728	0.82[CHB][hapmap]
rs13232181	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs1468338	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs17436977	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs1859482	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2107716	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs2270600	0.84[EUR][1000 genomes]
rs2270604	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286074	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs2291747	0.83[CEU][hapmap]
rs2394827	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394854	0.82[CEU][hapmap]
rs28566958	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28662014	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779193	0.82[CEU][hapmap]
rs3779194	0.82[CEU][hapmap]
rs3801254	0.82[CEU][hapmap]
rs3801255	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs3801256	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs3801263	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs3801264	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs3823740	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs4727388	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4727390	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729421	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729431	0.80[EUR][1000 genomes]
rs56098787	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61575270	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62479836	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62479838	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6465664	0.82[CHB][hapmap]
rs6465665	0.81[CHB][hapmap]
rs6465666	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6465667	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6465672	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6465675	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6465680	0.81[CEU][hapmap]
rs6465682	0.83[CEU][hapmap]
rs6944262	0.82[CEU][hapmap]
rs6945554	0.82[CHB][hapmap]
rs6947340	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6948540	0.83[CHB][hapmap]
rs6949718	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6951479	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955647	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6961129	0.88[CHB][hapmap]
rs6963210	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6967576	0.83[CEU][hapmap]
rs6968193	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs6970801	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6970990	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6975156	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs736753	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7458551	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs747631	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs747632	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7776638	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs7777415	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs7781916	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs7787309	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789380	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7796762	0.82[CHB][hapmap]
rs7797943	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7807455	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7807555	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs7812180	0.82[CEU][hapmap]
rs954050	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	esv1802449	chr7:97900191-97929668	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10249366	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs10249366	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97886600-97909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:97886800-97909200	Weak transcription	Brain Substantia Nigra	brain
3	chr7:97886800-97910000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:97887200-97910000	Weak transcription	Right Ventricle	heart
5	chr7:97887400-97908000	Weak transcription	Gastric	stomach
6	chr7:97887400-97910000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:97887600-97905800	Weak transcription	Left Ventricle	heart
8	chr7:97887600-97909600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:97888000-97908000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:97891000-97905200	Weak transcription	Liver	Liver
11	chr7:97891000-97909800	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:97891000-97909800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:97891200-97903200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:97891200-97909600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:97891200-97909800	Weak transcription	Aorta	Aorta
16	chr7:97891200-97909800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:97891400-97903000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:97891400-97905800	Weak transcription	Pancreas	Pancrea
19	chr7:97891400-97909600	Weak transcription	Primary B cells from cord blood	blood
20	chr7:97891400-97909800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:97892000-97903000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:97892000-97909600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:97892000-97909800	Weak transcription	Spleen	Spleen
24	chr7:97892600-97909600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:97893400-97905800	Weak transcription	Fetal Intestine Small	intestine
26	chr7:97893400-97909200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:97894600-97905800	Weak transcription	Lung	lung
28	chr7:97894800-97905800	Weak transcription	Fetal Stomach	stomach
29	chr7:97895600-97907800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:97895600-97910000	Weak transcription	HSMM	muscle
31	chr7:97895800-97909800	Weak transcription	Primary T cells from cord blood	blood
32	chr7:97895800-97910000	Weak transcription	Osteobl	bone
33	chr7:97896800-97908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:97896800-97908200	Weak transcription	HSMMtube	muscle
35	chr7:97896800-97909800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:97897000-97904400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:97897000-97905200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:97897000-97905800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:97897000-97907600	Weak transcription	Fetal Muscle Leg	muscle
40	chr7:97897000-97909800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:97897200-97907600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:97900000-97907800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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