Variant report

Variant	rs7944926
Chromosome Location	chr11:71165625-71165626
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	CTCF	chr11:71165500-71165650	GM12868	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:
2	chr11:71162324..71166430-chr11:71186520..71190924,4	K562	blood:
3	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
4	chr11:71163473..71165824-chr11:71289975..71292795,2	MCF-7	breast:

Variant related genes	Relation type
DHCR7	TF binding region
NADSYN1	TF binding region
ENSG00000172890	Chromatin interaction
ENSG00000249387	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000254682	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044482	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603330	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606631	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419334	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422045	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790010	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792306	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797951	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.80[ASN][1000 genomes]
rs12806844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12806918	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs12807718	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792229	0.82[TSI][hapmap]
rs1981412	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002064	0.82[TSI][hapmap]
rs2040323	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276362	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852853	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750997	0.95[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3794060	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4488226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944044	0.86[CHB][hapmap]
rs4944062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944949	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944956	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4944958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944996	0.89[ASN][1000 genomes]
rs4945008	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909217	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7944926	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs7944926	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs7944926	RNF121	cis	parietal	SCAN
rs7944926	NADSYN1	cis	Thyroid	GTEx
rs7944926	RAB6A	cis	cerebellum	SCAN
rs7944926	RP11-660L16.2	cis	lung	GTEx
rs7944926	NADSYN1	cis	Nerve Tibial	GTEx
rs7944926	RP11-660L16.2	cis	Stomach	GTEx
rs7944926	NADSYN1	cis	lung	GTEx
rs7944926	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs7944926	DHCR7	cis	cerebellum	SCAN
rs7944926	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs7944926	RP11-660L16.2	cis	Thyroid	GTEx
rs7944926	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7944926	RP11-660L16.2	cis	Artery Aorta	GTEx
rs7944926	RP11-660L16.2	cis	Whole Blood	GTEx
rs7944926	RP11-660L16.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71163000-71165800	Active TSS	Rectal Smooth Muscle	rectum
2	chr11:71164000-71165800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:71164400-71165800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:71164600-71165800	Flanking Active TSS	Dnd41	blood
5	chr11:71164800-71165800	Flanking Active TSS	Fetal Intestine Large	intestine
6	chr11:71164800-71165800	Enhancers	Spleen	Spleen
7	chr11:71164800-71166000	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr11:71164800-71166000	Enhancers	Fetal Brain Male	brain
9	chr11:71165000-71165800	Enhancers	Left Ventricle	heart
10	chr11:71165000-71165800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:71165000-71165800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr11:71165000-71166000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:71165000-71166000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:71165000-71166000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:71165000-71166200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:71165000-71166200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
18	chr11:71165200-71165800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:71165200-71165800	Enhancers	Primary T cells from cord blood	blood
20	chr11:71165200-71165800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:71165200-71165800	Enhancers	Fetal Brain Female	brain
22	chr11:71165200-71165800	Weak transcription	Fetal Stomach	stomach
23	chr11:71165200-71165800	Weak transcription	K562	blood
24	chr11:71165200-71165800	Enhancers	NH-A	brain
25	chr11:71165200-71166000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:71165200-71166000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:71165200-71166000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:71165200-71166000	Enhancers	Primary B cells from cord blood	blood
29	chr11:71165200-71166000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:71165200-71166000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr11:71165200-71166000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:71165200-71166000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:71165200-71166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:71165200-71166000	Enhancers	Liver	Liver
35	chr11:71165200-71166000	Weak transcription	Brain Anterior Caudate	brain
36	chr11:71165200-71166000	Enhancers	Brain Hippocampus Middle	brain
37	chr11:71165200-71166000	Enhancers	Colon Smooth Muscle	Colon
38	chr11:71165200-71166000	Enhancers	Gastric	stomach
39	chr11:71165200-71166000	Enhancers	Thymus	Thymus
40	chr11:71165200-71166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:71165200-71166200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:71165200-71166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:71165200-71166200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:71165200-71166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:71165200-71166200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:71165200-71166200	Enhancers	Primary B cells from peripheral blood	blood
47	chr11:71165200-71166200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr11:71165200-71166200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:71165200-71166200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr11:71165200-71166200	Weak transcription	Aorta	Aorta

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