Variant report

Variant	rs7759792
Chromosome Location	chr6:37924906-37924907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37924674..37926815-chr6:37929494..37931459,2	MCF-7	breast:
2	chr6:37920868..37922667-chr6:37923260..37925049,2	K562	blood:
3	chr6:37923129..37926098-chr6:37932741..37935067,3	MCF-7	breast:

Extended variants
information (count: 146 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10428769	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10485030	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10498739	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs10498740	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs10947702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947704	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947710	0.90[CHB][hapmap]
rs11750950	0.90[CHB][hapmap]
rs11751781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751927	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751962	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11752521	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752814	0.81[EUR][1000 genomes]
rs11752863	0.85[ASN][1000 genomes]
rs11753054	0.90[CHB][hapmap]
rs11753300	0.81[EUR][1000 genomes]
rs11755095	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11755629	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11756713	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11756902	0.90[CHB][hapmap]
rs11757072	0.90[CHB][hapmap]
rs11757161	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11758095	0.90[CHB][hapmap]
rs11759458	0.89[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs11759483	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap]
rs11759496	0.81[ASN][1000 genomes]
rs11759826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967129	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11969988	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12660221	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs12660498	0.83[CHB][hapmap]
rs12660732	0.85[CHB][hapmap]
rs12660773	0.82[CHB][hapmap]
rs12660919	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12660922	0.84[ASN][1000 genomes]
rs12661073	0.85[CHB][hapmap]
rs12661378	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12661480	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs12661702	0.82[ASN][1000 genomes]
rs12662305	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs12662426	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12663427	0.85[CHB][hapmap]
rs12664091	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12664768	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12664900	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap]
rs13190751	0.81[EUR][1000 genomes]
rs13195545	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13205214	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13205311	0.82[ASN][1000 genomes]
rs13206035	1.00[ASW][hapmap];0.94[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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16890177	0.85[CHB][hapmap]
rs16890181	0.85[CHB][hapmap]
rs16890185	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs16890215	0.85[CHB][hapmap]
rs16890247	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs16890267	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16890298	0.85[CHB][hapmap]
rs16890299	0.85[CHB][hapmap]
rs16890301	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16890305	0.85[CHB][hapmap]
rs16890307	0.81[CHB][hapmap]
rs16890309	0.85[CHB][hapmap]
rs16890362	0.85[CHB][hapmap]
rs16890370	0.85[CHB][hapmap]
rs1885324	0.84[CHB][hapmap]
rs2025431	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2055207	0.85[CHB][hapmap]
rs2064795	0.85[CHB][hapmap]
rs2103950	0.83[EUR][1000 genomes]
rs2145887	0.90[CHB][hapmap]
rs2273441	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274090	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs2274091	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395689	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2395692	0.90[CHB][hapmap]
rs2395693	0.90[CHB][hapmap]
rs2645111	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645125	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645130	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842510	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842511	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2842512	0.98[ASN][1000 genomes]
rs2842521	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34254045	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34450348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051126	0.99[ASN][1000 genomes]
rs35122358	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35216205	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35772972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35849984	0.87[EUR][1000 genomes]
rs3800364	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap]
rs3844314	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852216	0.85[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs4524602	0.85[CHB][hapmap]
rs55679841	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56023538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56129320	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57276677	0.82[ASN][1000 genomes]
rs57402213	0.81[ASN][1000 genomes]
rs57591988	0.81[ASN][1000 genomes]
rs57911756	0.82[ASN][1000 genomes]
rs58333612	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58611435	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59036086	0.83[ASN][1000 genomes]
rs59103990	0.84[ASN][1000 genomes]
rs59996041	0.81[ASN][1000 genomes]
rs61411293	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6458032	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903743	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6906289	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6908106	0.89[CEU][hapmap]
rs6910715	0.89[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6911716	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6936260	0.84[CEU][hapmap]
rs71569402	0.89[ASN][1000 genomes]
rs73419440	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73421436	0.85[ASN][1000 genomes]
rs73421439	0.85[ASN][1000 genomes]
rs752110	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7742226	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7745796	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7746266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7747996	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748312	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748392	0.90[CHB][hapmap]
rs7759145	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7761561	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7762052	0.84[CEU][hapmap]
rs7764130	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7773419	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7775794	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874095	0.85[CHB][hapmap]
rs876818	0.94[CHB][hapmap]
rs9470772	0.90[CHB][hapmap]
rs9470777	0.90[CHB][hapmap]
rs9470784	0.90[CHB][hapmap]
rs9470794	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9470798	0.90[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	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
rs7759792	KCTD20	cis	cerebellum	SCAN
rs7759792	BYSL	cis	cerebellum	SCAN
rs7759792	C6orf222	cis	cerebellum	SCAN
rs7759792	TMEM217	cis	parietal	SCAN
rs7759792	STK38	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
3	chr6:37887600-37933200	Weak transcription	NHDF-Ad	bronchial
4	chr6:37892600-37928800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:37896800-37929000	Weak transcription	Esophagus	oesophagus
6	chr6:37904800-37933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:37907000-37926600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:37911000-37933200	Weak transcription	NHEK	skin
9	chr6:37911600-37928600	Weak transcription	Lung	lung
10	chr6:37911600-37935400	Weak transcription	Primary B cells from cord blood	blood
11	chr6:37911600-37936200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:37917000-37928800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:37917800-37928600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:37918200-37926800	Weak transcription	Gastric	stomach
15	chr6:37920000-37933600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:37920600-37928000	Weak transcription	Primary T cells from cord blood	blood
17	chr6:37920600-37928000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:37920800-37930600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:37921000-37933000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:37921600-37925200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:37922200-37925800	Enhancers	Liver	Liver
22	chr6:37922200-37933400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:37922600-37925000	Enhancers	Left Ventricle	heart
24	chr6:37922600-37939000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:37922800-37925400	Enhancers	Adipose Nuclei	Adipose
26	chr6:37922800-37925600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:37922800-37928600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:37922800-37938600	Weak transcription	Fetal Lung	lung
29	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:37923000-37925200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr6:37923000-37926800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:37923000-37927000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:37923000-37928800	Weak transcription	Pancreas	Pancrea
35	chr6:37923000-37939000	Weak transcription	Ovary	ovary
36	chr6:37923200-37926800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:37923200-37928400	Weak transcription	Brain Angular Gyrus	brain
38	chr6:37923400-37925400	Enhancers	Brain Hippocampus Middle	brain
39	chr6:37923400-37925400	Enhancers	Brain Substantia Nigra	brain
40	chr6:37923400-37925600	Enhancers	Colon Smooth Muscle	Colon
41	chr6:37923400-37931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:37923600-37927800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:37923600-37938800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:37923600-37942200	Weak transcription	Aorta	Aorta
45	chr6:37923600-37947400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:37923800-37926400	Weak transcription	Small Intestine	intestine
47	chr6:37923800-37926600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:37923800-37926600	Weak transcription	GM12878-XiMat	blood
49	chr6:37923800-37926800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:37923800-37934200	Weak transcription	Fetal Muscle Leg	muscle

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