Variant report

Variant	rs11165012
Chromosome Location	chr1:94291481-94291482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94290941..94292978-chr1:94306774..94308364,2	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1004197	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874809	0.94[JPT][hapmap]
rs11164976	0.86[CHB][hapmap]
rs11164979	0.86[CHB][hapmap]
rs11164984	0.84[CHB][hapmap]
rs11164986	0.86[CHB][hapmap]
rs11165004	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11165006	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11165007	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11165016	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165030	0.94[JPT][hapmap]
rs11800779	0.86[CHB][hapmap]
rs12122176	0.81[JPT][hapmap]
rs12125068	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12125652	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12126518	0.86[CHB][hapmap]
rs12128353	0.86[CHB][hapmap]
rs12129080	0.86[CHB][hapmap]
rs12132181	0.86[CHB][hapmap]
rs12132405	0.86[CHB][hapmap]
rs12132569	0.86[CHB][hapmap]
rs12132625	0.86[CHB][hapmap]
rs12134159	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12135187	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12139561	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12139968	0.86[CHB][hapmap]
rs12140014	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12142384	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12144277	0.86[CHB][hapmap]
rs12240145	0.86[CHB][hapmap]
rs12402802	0.85[CHB][hapmap]
rs12405302	0.86[CHB][hapmap]
rs12406885	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12407244	0.86[CHB][hapmap]
rs12407550	0.86[CHB][hapmap]
rs12407732	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12407917	0.86[CHB][hapmap]
rs12408089	0.86[CHB][hapmap]
rs12408109	0.86[CHB][hapmap]
rs12408402	0.86[CHB][hapmap]
rs12408797	0.86[CHB][hapmap]
rs12410342	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12410985	0.92[CHB][hapmap]
rs12410986	0.86[CHB][hapmap]
rs12411043	0.85[CHB][hapmap]
rs12411056	0.86[CHB][hapmap]
rs12725087	0.86[CHB][hapmap]
rs12745888	0.86[CHB][hapmap]
rs17100392	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1848	0.86[CHB][hapmap]
rs1852	0.83[CHB][hapmap]
rs1980084	0.86[CHB][hapmap]
rs2179908	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2391313	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3170633	0.82[JPT][hapmap]
rs3761912	0.94[JPT][hapmap]
rs3935320	0.86[CHB][hapmap]
rs3935334	0.86[CHB][hapmap]
rs4075343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs4281327	0.86[CHB][hapmap]
rs4348734	0.86[CHB][hapmap]
rs4354545	0.86[CHB][hapmap]
rs4357541	0.86[CHB][hapmap]
rs6541395	0.86[CHB][hapmap]
rs6541396	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661992	0.93[EUR][1000 genomes]
rs6662311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679619	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6684128	0.86[CHB][hapmap]
rs6684389	0.86[CHB][hapmap]
rs6687387	0.94[JPT][hapmap]
rs6687914	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688926	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6692107	0.86[CHB][hapmap]
rs6692717	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs717912	0.86[CHB][hapmap]
rs7515191	0.94[JPT][hapmap]
rs7515462	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7517826	0.94[JPT][hapmap]
rs7521365	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533596	0.94[JPT][hapmap]
rs7536914	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7537445	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7544883	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7546315	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7547179	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7549683	0.94[JPT][hapmap]
rs7552104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs960625	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9729722	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
4	esv1003322	chr1:94285785-94294520	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3319346	chr1:94286364-94293162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3513622	chr1:94287264-94292362	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3319347	chr1:94287389-94292237	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3513620	chr1:94287664-94292262	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3319348	chr1:94287864-94291762	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3453869	chr1:94287918-94292127	Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3453870	chr1:94287918-94292127	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3513621	chr1:94288147-94292147	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv8088	chr1:94288193-94291497	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv821520	chr1:94288287-94291584	Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv823542	chr1:94288287-94291584	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv1819009	chr1:94288463-94291481	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1820927	chr1:94288463-94291481	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv1829117	chr1:94288463-94291481	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv1832819	chr1:94288463-94291481	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv1814087	chr1:94288524-94291481	Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv1818062	chr1:94288524-94291481	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv546830	chr1:94288524-94291481	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv546831	chr1:94288524-94294190	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv546832	chr1:94288524-94294492	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	esv1831177	chr1:94288524-94304239	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11165012	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs11165012	GCLM	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:94283600-94293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94284000-94294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:94284200-94292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:94284200-94306200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:94284400-94296000	Weak transcription	Fetal Intestine Small	intestine
9	chr1:94286400-94294800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:94286600-94295600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:94287000-94292400	Weak transcription	HUVEC	blood vessel
12	chr1:94287400-94293600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:94287600-94292600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:94287600-94292800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:94287600-94292800	Weak transcription	A549	lung
16	chr1:94287600-94292800	Weak transcription	HSMM	muscle
17	chr1:94287600-94292800	Weak transcription	HSMMtube	muscle
18	chr1:94287600-94292800	Weak transcription	NH-A	brain
19	chr1:94287600-94293200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:94287600-94294000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:94287800-94292800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:94288200-94293200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:94288800-94292400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:94288800-94292400	Weak transcription	NHDF-Ad	bronchial
25	chr1:94288800-94292800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:94288800-94293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:94289000-94292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:94289000-94292800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:94289000-94293000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:94289000-94293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:94289000-94293200	Weak transcription	NHEK	skin
32	chr1:94289200-94292800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:94289600-94292000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:94289600-94292600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:94290000-94296400	Enhancers	Placenta	Placenta
36	chr1:94290200-94311400	Weak transcription	Aorta	Aorta
37	chr1:94290600-94291800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:94290600-94292600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:94290600-94293200	Weak transcription	HMEC	breast
40	chr1:94290800-94293400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:94291200-94294800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:94291400-94291800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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