Variant report

Variant	rs35850374
Chromosome Location	chr7:65357776-65357777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10229450	0.81[EUR][1000 genomes]
rs10279841	0.84[EUR][1000 genomes]
rs10807697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1167385	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1167386	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11763147	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs11768292	0.80[ASN][1000 genomes]
rs11770828	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs12670952	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13237956	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1631091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1701751	0.82[EUR][1000 genomes]
rs1701757	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1701760	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1723268	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1723275	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1829943	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1880556	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1917563	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2008188	0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462573	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2658585	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2658587	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2690442	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2692056	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2939548	0.81[AMR][1000 genomes]
rs2946579	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2949690	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2949692	0.83[EUR][1000 genomes]
rs3201569	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34973832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35135885	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4467826	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717271	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4718286	0.81[AMR][1000 genomes]
rs4718288	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55773927	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55796207	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56028712	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62470893	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66552782	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6945322	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6954920	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6955582	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6960048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs709604	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs736270	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7383796	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7784623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7791814	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809991	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs781143	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781144	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781145	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs781152	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9530	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv1029800	chr7:65309327-65367692	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised 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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs35850374	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs35850374	ERV3	cis	cerebellum	SCAN
rs35850374	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs35850374	ZNF273	cis	cerebellum	SCAN
rs35850374	RP4-756H11.3	cis	lung	GTEx
rs35850374	CRCP	cis	parietal	SCAN
rs35850374	GUSB	cis	parietal	SCAN
rs35850374	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs35850374	ERV3	cis	parietal	SCAN
rs35850374	RP4-756H11.3	cis	Artery Aorta	GTEx
rs35850374	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs35850374	RP4-756H11.3	cis	Artery Tibial	GTEx
rs35850374	RP4-756H11.3	cis	Thyroid	GTEx
rs35850374	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs35850374	KCTD7	cis	parietal	SCAN
rs35850374	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs35850374	CRCP	cis	cerebellum	SCAN
rs35850374	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs35850374	GUSB	cis	lymphoblastoid	seeQTL
rs35850374	GUSB	cis	cerebellum	SCAN
rs35850374	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs35850374	RABGEF1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65339200-65372200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:65339400-65366200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:65339400-65366200	Weak transcription	Fetal Intestine Small	intestine
4	chr7:65339400-65371800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:65339600-65360000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr7:65339600-65364000	Weak transcription	Left Ventricle	heart
7	chr7:65339600-65366000	Weak transcription	NHEK	skin
8	chr7:65339600-65366200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:65339600-65366200	Weak transcription	Fetal Stomach	stomach
10	chr7:65339600-65366400	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:65339600-65366800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:65339600-65368600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:65339600-65370000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:65339600-65371600	Weak transcription	Thymus	Thymus
15	chr7:65339600-65381200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:65339600-65394400	Weak transcription	HMEC	breast
17	chr7:65340000-65370200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:65345200-65419000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:65345800-65367600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:65347000-65359200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr7:65349400-65364000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:65349600-65367400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:65349600-65368400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:65350200-65367200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:65351600-65359200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:65351600-65366600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:65351800-65389200	Weak transcription	Lung	lung
28	chr7:65353000-65371600	Weak transcription	Liver	Liver
29	chr7:65353200-65371200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:65353400-65367600	Weak transcription	Fetal Intestine Large	intestine
31	chr7:65353600-65358400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:65353600-65362600	Weak transcription	Fetal Kidney	kidney
33	chr7:65354000-65361600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:65354000-65363800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:65354000-65366400	Weak transcription	Psoas Muscle	Psoas
36	chr7:65354000-65369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:65354200-65360200	Weak transcription	Aorta	Aorta
38	chr7:65354200-65367200	Weak transcription	Fetal Brain Female	brain
39	chr7:65355200-65358000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:65355400-65358000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:65355600-65358000	Strong transcription	Dnd41	blood
42	chr7:65355600-65358400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:65355800-65357800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:65355800-65358400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:65356000-65358600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:65356000-65359400	Weak transcription	HUVEC	blood vessel
47	chr7:65356200-65358000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:65356200-65358200	Strong transcription	Primary T cells from cord blood	blood
49	chr7:65356200-65358200	Strong transcription	Fetal Thymus	thymus
50	chr7:65356400-65358000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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