Variant report

Variant	rs6913530
Chromosome Location	chr6:36598209-36598210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36597486..36599707-chr6:36615187..36618681,3	MCF-7	breast:
2	chr6:36560968..36563809-chr6:36597718..36600629,3	K562	blood:
3	chr12:120728269..120730089-chr6:36597949..36599449,2	K562	blood:
4	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10214849	0.83[CHD][hapmap]
rs1061632	0.81[CEU][hapmap]
rs1076931	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807169	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947613	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs10947614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755264	0.81[CEU][hapmap]
rs11756557	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756969	0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs11757842	0.81[CEU][hapmap]
rs1191	0.81[CEU][hapmap]
rs12153820	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190062	0.81[CEU][hapmap]
rs12202732	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12208086	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12211825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1535510	0.81[CEU][hapmap]
rs16888552	0.81[CEU][hapmap]
rs1812018	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1812019	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1812020	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983781	0.81[CEU][hapmap]
rs2001101	0.97[EUR][1000 genomes]
rs2007741	0.81[CEU][hapmap]
rs2145048	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146333	0.80[CEU][hapmap]
rs2187827	0.81[CEU][hapmap]
rs2239807	0.81[CEU][hapmap]
rs2239808	0.81[CEU][hapmap]
rs2300064	0.81[CEU][hapmap]
rs3798473	0.81[CEU][hapmap]
rs3819760	0.81[CEU][hapmap]
rs4598	0.81[CEU][hapmap]
rs56144242	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61211228	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457920	0.81[CEU][hapmap]
rs6457923	0.81[CEU][hapmap]
rs6457928	0.81[CEU][hapmap]
rs6457929	0.81[CEU][hapmap]
rs6899372	0.80[CEU][hapmap]
rs6905347	0.81[CEU][hapmap]
rs6905686	0.81[CEU][hapmap]
rs6911877	0.81[CEU][hapmap]
rs6912982	0.81[CEU][hapmap]
rs6913613	0.81[CEU][hapmap]
rs6913714	0.81[CEU][hapmap]
rs6917951	0.80[CEU][hapmap]
rs6920166	0.81[CEU][hapmap]
rs6926522	0.81[CEU][hapmap]
rs6927896	0.81[CEU][hapmap]
rs6928087	0.80[CEU][hapmap]
rs6936942	0.81[CEU][hapmap]
rs6941593	0.81[CEU][hapmap]
rs72852338	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72852340	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73410251	0.81[ASN][1000 genomes]
rs7344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741888	0.86[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7743396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7747264	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7755461	0.86[JPT][hapmap]
rs7759778	0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759933	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7760766	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7767296	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7772524	0.81[CEU][hapmap]
rs9296193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs933236	0.81[CEU][hapmap]
rs9349001	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357217	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9357218	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357219	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366907	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9366908	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9366909	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368938	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368939	0.94[EUR][1000 genomes]
rs9368940	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368943	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380577	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380578	0.83[EUR][1000 genomes]
rs9380580	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380582	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394359	0.83[EUR][1000 genomes]
rs9394360	0.82[EUR][1000 genomes]
rs9394361	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394362	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394363	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394365	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470280	0.81[CEU][hapmap]
rs9470294	0.81[CEU][hapmap]
rs9470295	0.81[CEU][hapmap]
rs9470297	0.81[CEU][hapmap]
rs9470300	0.81[CEU][hapmap]
rs9470302	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6913530	GLO1	cis	cerebellum	SCAN
rs6913530	TULP1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36580200-36599200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:36581400-36604400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:36582800-36610800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:36593400-36599200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:36593400-36601600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:36593600-36599000	Weak transcription	A549	lung
7	chr6:36593600-36601800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:36593800-36601400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:36595200-36598400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr6:36595600-36598400	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:36595600-36601800	Weak transcription	Lung	lung
12	chr6:36595800-36598800	Weak transcription	Fetal Heart	heart
13	chr6:36595800-36599000	Weak transcription	HSMMtube	muscle
14	chr6:36595800-36599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:36595800-36601000	Weak transcription	Stomach Mucosa	stomach
16	chr6:36595800-36601200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:36595800-36601200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:36595800-36601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:36595800-36601800	Weak transcription	Fetal Thymus	thymus
20	chr6:36595800-36601800	Weak transcription	Right Ventricle	heart
21	chr6:36595800-36602000	Weak transcription	Gastric	stomach
22	chr6:36596000-36598600	Enhancers	GM12878-XiMat	blood
23	chr6:36596000-36599000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:36596000-36599200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:36596000-36599200	Weak transcription	Left Ventricle	heart
26	chr6:36596000-36601200	Weak transcription	Fetal Lung	lung
27	chr6:36596000-36601200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:36596000-36601600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:36596000-36602000	Weak transcription	HSMM	muscle
30	chr6:36597000-36603000	Enhancers	Fetal Muscle Leg	muscle
31	chr6:36597200-36599200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:36597200-36601200	Weak transcription	Colonic Mucosa	Colon
33	chr6:36597200-36601600	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:36597400-36599200	Weak transcription	Placenta	Placenta
35	chr6:36597400-36601000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:36597400-36601000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:36597400-36601200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:36597400-36601200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:36597400-36601200	Weak transcription	Pancreas	Pancrea
40	chr6:36597400-36601200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:36597400-36601200	Weak transcription	HUVEC	blood vessel
42	chr6:36597400-36601400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:36597400-36601600	Weak transcription	Right Atrium	heart
44	chr6:36597400-36601800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:36597400-36601800	Weak transcription	Brain Substantia Nigra	brain
46	chr6:36597400-36601800	Weak transcription	Ovary	ovary
47	chr6:36597400-36602000	Weak transcription	Fetal Kidney	kidney
48	chr6:36597600-36599000	Weak transcription	Fetal Stomach	stomach
49	chr6:36597600-36601400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:36597600-36601400	Weak transcription	Adipose Nuclei	Adipose

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