Variant report

Variant	rs6965800
Chromosome Location	chr7:4011331-4011332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10227007	0.83[CEU][hapmap]
rs10230104	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[TSI][hapmap]
rs10260999	0.83[ASN][1000 genomes]
rs10277771	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11974050	0.94[ASN][1000 genomes]
rs11977815	0.90[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs12534781	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12701279	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12701280	0.90[CHB][hapmap]
rs12701282	0.82[CHB][hapmap]
rs12701284	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[TSI][hapmap]
rs12701287	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs12701291	0.87[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs12701296	0.87[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12701305	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12701311	0.87[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12701325	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17134054	0.81[CEU][hapmap]
rs17134098	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010279	0.82[CHB][hapmap]
rs2016180	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes]
rs2044224	0.80[YRI][hapmap];0.84[AMR][1000 genomes]
rs2068368	0.87[CEU][hapmap];0.87[CHD][hapmap];0.90[TSI][hapmap]
rs2120331	0.86[ASN][1000 genomes]
rs3801066	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801067	0.82[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs4720116	0.83[AMR][1000 genomes]
rs4720128	0.81[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723267	0.90[CHB][hapmap]
rs4723268	0.82[CEU][hapmap]
rs4723269	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[TSI][hapmap]
rs4723270	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs4723275	0.83[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap]
rs4723277	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs4723284	0.80[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes]
rs62439587	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6462476	0.83[CEU][hapmap]
rs6462500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951851	0.82[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes]
rs6955390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969705	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6974821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6978757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776705	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7784194	0.83[CEU][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs7786879	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7789580	0.83[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.81[TSI][hapmap]
rs7801639	0.88[MEX][hapmap];0.86[TSI][hapmap]
rs7805988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs968689	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1019086	chr7:3968656-4044519	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538687	chr7:3968656-4044519	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1033687	chr7:4006020-4267871	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv538688	chr7:4006020-4267871	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6965800	WIPI2	cis	parietal	SCAN
rs6965800	MAFK	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3988600-4032600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr7:3989200-4013800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:3989400-4031000	Weak transcription	Right Ventricle	heart
4	chr7:3989800-4020800	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:3996200-4017200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:3996400-4015800	Weak transcription	HSMM	muscle
7	chr7:3996400-4037600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:3997000-4019400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:3998000-4020800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:3998400-4045600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:4000200-4016200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:4000200-4032600	Weak transcription	Adipose Nuclei	Adipose
13	chr7:4001600-4013000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:4001800-4014600	Weak transcription	Fetal Intestine Large	intestine
15	chr7:4001800-4016800	Weak transcription	Fetal Brain Male	brain
16	chr7:4001800-4016800	Weak transcription	Fetal Kidney	kidney
17	chr7:4002000-4014000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:4002400-4014200	Weak transcription	Fetal Brain Female	brain
19	chr7:4002400-4016600	Weak transcription	Fetal Muscle Leg	muscle
20	chr7:4004800-4011600	Weak transcription	Fetal Intestine Small	intestine
21	chr7:4005800-4012200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:4006000-4014000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:4007200-4012200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:4007800-4027200	Weak transcription	Spleen	Spleen
25	chr7:4008000-4016800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:4008000-4020600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:4008000-4021600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr7:4008000-4030400	Weak transcription	Gastric	stomach
29	chr7:4008200-4020800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:4008600-4015200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:4009200-4014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:4009200-4014000	Weak transcription	Fetal Stomach	stomach
33	chr7:4009200-4014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:4010200-4011600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:4010200-4016200	Weak transcription	Ovary	ovary
36	chr7:4010400-4011400	Strong transcription	Aorta	Aorta
37	chr7:4010600-4012000	Weak transcription	Fetal Lung	lung
38	chr7:4010800-4011400	Strong transcription	Pancreas	Pancrea
39	chr7:4011000-4011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:4011200-4013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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