Variant report

Variant	rs10078304
Chromosome Location	chr5:94027011-94027012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:94026982-94027087	HUVEC	blood vessel:	n/a	n/a
2	NFIC	chr5:94026880-94027513	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr5:94026912-94027417	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr5:94026844-94027459	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ANKRD32	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10035632	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10035650	1.00[CHB][hapmap]
rs10037228	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10039801	1.00[CHB][hapmap]
rs10041262	0.87[ASN][1000 genomes]
rs10041551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041843	0.87[ASN][1000 genomes]
rs10043779	1.00[CHB][hapmap]
rs10044797	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs10056685	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10058130	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10058618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059194	1.00[CHB][hapmap]
rs10061737	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062248	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070258	0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10076188	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076461	0.87[ASN][1000 genomes]
rs10078049	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476612	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs10476613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476615	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949227	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955373	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960129	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516225	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12517866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12518034	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs12522312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13169956	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353994	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354061	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13358642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13362556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17083818	1.00[CHB][hapmap]
rs28645132	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787271	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs306573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306575	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869218	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55974730	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6862592	0.87[ASN][1000 genomes]
rs6873364	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879307	0.82[EUR][1000 genomes]
rs755898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705424	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7725095	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725698	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731360	0.89[EUR][1000 genomes]
rs7737779	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs9314117	0.83[ASW][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.80[YRI][hapmap]
rs9314118	0.81[EUR][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	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10078304	ARSK	cis	parietal	SCAN
rs10078304	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs10078304	ANKRD32	cis	multi-tissue	Pritchard
rs10078304	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10078304	C5orf36	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955800-94027600	Weak transcription	NH-A	brain
2	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
4	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:93994400-94027600	Weak transcription	Liver	Liver
6	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
7	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
9	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
10	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
13	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
15	chr5:93996200-94029800	Weak transcription	Ovary	ovary
16	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:93996600-94048400	Weak transcription	Lung	lung
18	chr5:93996800-94036200	Weak transcription	Gastric	stomach
19	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
20	chr5:94001000-94030000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:94001800-94027600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:94008800-94027600	Weak transcription	Osteobl	bone
24	chr5:94010600-94027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:94010800-94027600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:94010800-94027800	Weak transcription	NHLF	lung
27	chr5:94011000-94027800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:94011000-94027800	Weak transcription	HUVEC	blood vessel
29	chr5:94011400-94029000	Weak transcription	Fetal Heart	heart
30	chr5:94012600-94027200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:94012600-94027600	Weak transcription	HSMM	muscle
32	chr5:94012600-94027800	Weak transcription	NHEK	skin
33	chr5:94012600-94034000	Weak transcription	Pancreas	Pancrea
34	chr5:94012600-94035000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
36	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
38	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:94013000-94032400	Weak transcription	HepG2	liver
41	chr5:94013200-94027600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
43	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:94021200-94028200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:94021600-94028200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr5:94021800-94027800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:94022200-94028000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:94022200-94029800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:94022400-94028600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:94022800-94028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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