Variant report

Variant	rs4576
Chromosome Location	chr11:66331000-66331001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66324925..66326614-chr11:66329885..66331523,2	MCF-7	breast:
2	chr11:66328947..66331714-chr11:66414609..66416864,2	K562	blood:
3	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
4	chr11:66329216..66333273-chr11:66381522..66384587,4	K562	blood:
5	chr11:66330753..66332695-chr11:66333355..66336116,2	K562	blood:

Variant related genes	Relation type
ENSG00000174080	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000199325	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10501397	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896124	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896129	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11227495	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227497	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227498	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227499	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227500	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227501	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227502	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227503	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227509	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227510	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227511	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227512	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227514	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227515	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227522	0.88[EUR][1000 genomes]
rs11227523	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227525	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227527	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11550299	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11821155	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11822028	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11822099	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11824771	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12099041	0.90[EUR][1000 genomes]
rs12221821	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12223479	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12272545	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17065	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17147644	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17495838	1.00[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs17496250	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17496586	0.95[EUR][1000 genomes]
rs17580784	0.84[EUR][1000 genomes]
rs2075792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276406	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277302	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2279864	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2279865	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2298806	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305532	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305533	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305534	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305535	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28414721	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3179961	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35733139	0.87[EUR][1000 genomes]
rs3737525	1.00[CEU][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3741360	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816492	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3819247	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825065	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3892818	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4542420	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4630309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930182	0.84[EUR][1000 genomes]
rs4930183	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930377	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930378	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930379	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930380	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs506028	0.94[JPT][hapmap]
rs519380	0.91[GIH][hapmap];0.93[MEX][hapmap]
rs56144989	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57045447	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57207756	0.95[EUR][1000 genomes]
rs57288351	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57596493	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57634456	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57691879	0.90[EUR][1000 genomes]
rs57724777	0.90[EUR][1000 genomes]
rs59829960	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59982644	0.98[EUR][1000 genomes]
rs60358007	0.87[EUR][1000 genomes]
rs60645853	0.98[EUR][1000 genomes]
rs61561111	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61582507	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7104378	0.84[EUR][1000 genomes]
rs7116921	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7116940	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7123176	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7928882	0.87[EUR][1000 genomes]
rs7939759	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7943327	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7950407	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7950790	0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][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	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4576	CCND1	cis	parietal	SCAN
rs4576	PACS1	cis	parietal	SCAN
rs4576	CCS	cis	cerebellum	SCAN
rs4576	CTSF	cis	parietal	SCAN
rs4576	SPTBN2	cis	cerebellum	SCAN
rs4576	BBS1	cis	parietal	SCAN
rs4576	CDC42EP2	cis	cerebellum	SCAN
rs4576	ESRRA	cis	cerebellum	SCAN
rs4576	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs4576	UNC93B1	cis	cerebellum	SCAN
rs4576	PRDX5	cis	cerebellum	SCAN
rs4576	BBS1	cis	cerebellum	SCAN
rs4576	CTSF	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr11:66326600-66331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:66326600-66334800	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:66326800-66331200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:66326800-66331200	Weak transcription	Right Ventricle	heart
8	chr11:66326800-66331400	Weak transcription	Liver	Liver
9	chr11:66326800-66334800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:66326800-66334800	Weak transcription	Pancreas	Pancrea
11	chr11:66326800-66335000	Weak transcription	Psoas Muscle	Psoas
12	chr11:66326800-66335000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:66326800-66335200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:66326800-66335200	Weak transcription	Esophagus	oesophagus
15	chr11:66326800-66335200	Weak transcription	Left Ventricle	heart
16	chr11:66326800-66335200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:66327000-66332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:66327000-66333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:66327000-66335200	Weak transcription	Fetal Heart	heart
20	chr11:66327200-66332200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:66327200-66333200	Weak transcription	Lung	lung
22	chr11:66327200-66335000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:66327400-66331800	Weak transcription	Placenta	Placenta
24	chr11:66327400-66334600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:66327400-66335200	Weak transcription	Right Atrium	heart
26	chr11:66327600-66332200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:66327800-66331200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:66327800-66332000	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr11:66328000-66333000	Strong transcription	Fetal Muscle Leg	muscle
30	chr11:66328000-66334000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:66328000-66334400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:66328000-66335000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:66328200-66331800	Weak transcription	Gastric	stomach
34	chr11:66328200-66333600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:66328400-66334800	Strong transcription	Fetal Stomach	stomach
36	chr11:66329000-66331200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:66329000-66334200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:66329000-66334600	Strong transcription	Brain Angular Gyrus	brain
39	chr11:66329000-66335000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:66329400-66331200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:66329400-66331400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:66329400-66333800	Strong transcription	Adipose Nuclei	Adipose
43	chr11:66329400-66333800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:66329400-66334200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:66329400-66334400	Strong transcription	Brain Hippocampus Middle	brain
46	chr11:66329400-66334800	Strong transcription	Brain Germinal Matrix	brain
47	chr11:66329400-66336600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:66329600-66332400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:66329600-66333800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:66329600-66333800	Strong transcription	Brain Substantia Nigra	brain

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