Variant report

Variant	rs6692717
Chromosome Location	chr1:94283093-94283094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94280000..94282465-chr1:94282888..94285001,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1004197	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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]
rs11165012	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165016	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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];0.99[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	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661992	0.95[EUR][1000 genomes]
rs6662311	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679619	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684128	0.86[CHB][hapmap]
rs6684389	0.86[CHB][hapmap]
rs6687387	0.94[JPT][hapmap]
rs6687914	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688926	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6692107	0.86[CHB][hapmap]
rs6702162	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717912	0.86[CHB][hapmap]
rs7515191	0.94[JPT][hapmap]
rs7515462	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7517826	0.94[JPT][hapmap]
rs7521365	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533596	0.94[JPT][hapmap]
rs7536914	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537445	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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];0.98[EUR][1000 genomes]
rs960625	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9729722	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	esv1005153	chr1:94281705-94283362	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6692717	GCLM	cis	parietal	SCAN
rs6692717	LRRC8B	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
2	chr1:94275800-94285000	Enhancers	HMEC	breast
3	chr1:94276000-94283600	Enhancers	HSMM	muscle
4	chr1:94276000-94285200	Enhancers	Placenta	Placenta
5	chr1:94276800-94283800	Enhancers	NHEK	skin
6	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:94277600-94284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:94278600-94283200	Enhancers	Osteobl	bone
10	chr1:94278600-94284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:94279400-94284400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:94279800-94284400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:94279800-94284600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:94280000-94285600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:94280000-94290000	Weak transcription	Brain Angular Gyrus	brain
17	chr1:94280200-94284000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:94280400-94285000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:94280800-94283200	Enhancers	HSMMtube	muscle
20	chr1:94280800-94283400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:94280800-94285800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:94281000-94284400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:94281200-94283400	Enhancers	NH-A	brain
24	chr1:94281200-94284800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:94281200-94289600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:94281400-94285000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:94281400-94285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:94281400-94285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:94281600-94285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:94281600-94285400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:94281800-94284200	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:94281800-94285600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:94282200-94283200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:94282200-94284200	Enhancers	Adipose Nuclei	Adipose
35	chr1:94282200-94284200	Enhancers	Dnd41	blood
36	chr1:94282200-94284400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:94282200-94284400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:94282400-94283200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:94282400-94283200	Enhancers	Fetal Lung	lung
40	chr1:94282400-94283200	Enhancers	A549	lung
41	chr1:94282400-94283200	Enhancers	HepG2	liver
42	chr1:94282400-94283600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr1:94282400-94283600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:94282400-94283600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:94282400-94283600	Enhancers	Right Atrium	heart
46	chr1:94282400-94283800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:94282400-94284000	Enhancers	Primary T cells from cord blood	blood
48	chr1:94282400-94284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:94282400-94284000	Enhancers	Liver	Liver
50	chr1:94282400-94284200	Enhancers	Primary T cells fromperipheralblood	blood

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