Variant report

Variant	rs6485597
Chromosome Location	chr11:45186029-45186030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45179374..45181360-chr11:45184809..45187751,2	K562	blood:
2	chr11:45167897..45170381-chr11:45182910..45186280,3	MCF-7	breast:
3	chr11:45184562..45186695-chr11:45200479..45203077,3	MCF-7	breast:
4	chr11:45173610..45176134-chr11:45184836..45187202,2	K562	blood:
5	chr11:45184515..45187339-chr11:45200209..45203185,3	MCF-7	breast:
6	chr11:45184640..45186467-chr11:45245800..45248700,2	MCF-7	breast:
7	chr11:45167891..45170733-chr11:45184381..45188024,4	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10742743	0.86[JPT][hapmap]
rs10742744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10742745	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742746	0.87[ASN][1000 genomes]
rs1078930	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838425	0.86[JPT][hapmap]
rs10838426	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038356	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11038361	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12281438	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2863159	0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3758722	1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3758728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3781706	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4755948	0.95[EUR][1000 genomes]
rs4755953	0.86[JPT][hapmap]
rs6416128	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6485594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485599	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485601	0.95[EUR][1000 genomes]
rs6485602	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs746555	0.95[EUR][1000 genomes]
rs7937949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942214	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942347	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7945018	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45169800-45188000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:45170000-45190000	Weak transcription	Primary B cells from cord blood	blood
3	chr11:45172400-45190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:45175600-45186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:45176000-45186600	Genic enhancers	Fetal Stomach	stomach
6	chr11:45178200-45187600	Enhancers	Fetal Heart	heart
7	chr11:45178800-45186800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr11:45180000-45193000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:45181600-45193600	Weak transcription	Fetal Intestine Large	intestine
10	chr11:45182000-45187200	Enhancers	Brain Angular Gyrus	brain
11	chr11:45182200-45186600	Enhancers	Fetal Muscle Trunk	muscle
12	chr11:45182200-45186800	Enhancers	Brain Hippocampus Middle	brain
13	chr11:45182200-45187200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr11:45182400-45186400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:45182400-45187000	Enhancers	Right Ventricle	heart
16	chr11:45182400-45187400	Enhancers	Ovary	ovary
17	chr11:45183000-45186800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr11:45183200-45186600	Enhancers	Fetal Brain Female	brain
19	chr11:45183600-45186600	Enhancers	Brain Germinal Matrix	brain
20	chr11:45183600-45186800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:45183600-45200400	Weak transcription	Esophagus	oesophagus
22	chr11:45183800-45186200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:45183800-45187400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:45183800-45188200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:45183800-45190400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:45183800-45190800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:45183800-45201200	Weak transcription	Gastric	stomach
28	chr11:45184200-45188400	Strong transcription	Fetal Intestine Small	intestine
29	chr11:45184200-45190000	Weak transcription	Fetal Lung	lung
30	chr11:45184400-45186400	Enhancers	Left Ventricle	heart
31	chr11:45184400-45186400	Enhancers	Right Atrium	heart
32	chr11:45184600-45186600	Enhancers	HSMMtube	muscle
33	chr11:45184600-45187600	Enhancers	Fetal Brain Male	brain
34	chr11:45184600-45188000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:45184800-45190000	Weak transcription	Pancreas	Pancrea
36	chr11:45185000-45186400	Enhancers	Colon Smooth Muscle	Colon
37	chr11:45185000-45186800	Enhancers	Primary hematopoietic stem cells	blood
38	chr11:45185000-45187200	Enhancers	Aorta	Aorta
39	chr11:45185200-45186200	Enhancers	Psoas Muscle	Psoas
40	chr11:45185200-45186600	Genic enhancers	Fetal Muscle Leg	muscle
41	chr11:45185200-45186600	Enhancers	NH-A	brain
42	chr11:45185400-45186400	Enhancers	Brain Anterior Caudate	brain
43	chr11:45185400-45186600	Enhancers	HSMM	muscle
44	chr11:45185400-45187000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:45185600-45186200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:45185600-45186200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:45185600-45186200	Enhancers	HMEC	breast
48	chr11:45185600-45186400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
49	chr11:45185600-45186400	Enhancers	Osteobl	bone
50	chr11:45185600-45190000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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