Variant report

Variant	rs15677
Chromosome Location	chr11:107977489-107977490
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	chr11:107960048..107962789-chr11:107975595..107977973,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPAT-2	chr11:107977428-107977525	ENSG00000255467.1

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10789652	0.87[EUR][1000 genomes]
rs10890810	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212486	0.86[EUR][1000 genomes]
rs11212490	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11212512	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11604711	1.00[JPT][hapmap]
rs11607588	0.82[CHB][hapmap]
rs11823929	0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs12270224	0.88[EUR][1000 genomes]
rs12277368	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12416788	1.00[JPT][hapmap]
rs12418162	1.00[CHB][hapmap]
rs12418673	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12421527	1.00[JPT][hapmap]
rs12793438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12796482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12803043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17679325	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2271853	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs35583347	0.91[EUR][1000 genomes]
rs3858392	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3908131	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4753827	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs56214765	0.91[EUR][1000 genomes]
rs67456286	0.92[EUR][1000 genomes]
rs7104942	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7105163	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7106930	0.93[EUR][1000 genomes]
rs7120705	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7121568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7122356	0.85[EUR][1000 genomes]
rs7949655	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107908400-107980600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:107928200-107985200	Weak transcription	Psoas Muscle	Psoas
3	chr11:107946600-107986000	Weak transcription	Brain Angular Gyrus	brain
4	chr11:107953200-107991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:107953600-107986000	Weak transcription	Pancreas	Pancrea
6	chr11:107955800-107991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:107958600-107978200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:107958800-107980400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:107959200-107977800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:107961400-107977800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:107962800-107977600	Weak transcription	Esophagus	oesophagus
12	chr11:107964000-107978600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:107964600-107978000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:107966200-107982200	Weak transcription	Spleen	Spleen
15	chr11:107966200-107986000	Weak transcription	Brain Substantia Nigra	brain
16	chr11:107966400-107992000	Weak transcription	Fetal Brain Male	brain
17	chr11:107966600-107986000	Weak transcription	HMEC	breast
18	chr11:107967000-107991400	Weak transcription	A549	lung
19	chr11:107968200-107986000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:107968200-107986800	Weak transcription	Colonic Mucosa	Colon
21	chr11:107968200-107992000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:107968600-107978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:107968600-107986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:107969000-107991600	Weak transcription	Hela-S3	cervix
25	chr11:107969200-107978200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:107969200-107986000	Weak transcription	NHLF	lung
27	chr11:107969200-107986200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:107969200-107991800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:107970400-107979400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:107970600-107991600	Weak transcription	HepG2	liver
31	chr11:107972200-107986000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:107972400-107985000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:107972400-107986400	Weak transcription	NHEK	skin
34	chr11:107972400-107991400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:107972400-107991600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:107972400-107992000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:107972600-107978000	Weak transcription	Fetal Heart	heart
38	chr11:107972600-107980000	Weak transcription	HSMMtube	muscle
39	chr11:107972600-107985400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:107972600-107992200	Weak transcription	Gastric	stomach
41	chr11:107973200-107986400	Weak transcription	Ovary	ovary
42	chr11:107973400-107991800	Weak transcription	Primary T cells from cord blood	blood
43	chr11:107973600-107985600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:107973600-107985600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:107973600-107986000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:107973600-107986000	Weak transcription	NH-A	brain
47	chr11:107973600-107991600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:107973600-107991800	Weak transcription	Primary B cells from cord blood	blood
49	chr11:107973600-107991800	Weak transcription	Brain Germinal Matrix	brain
50	chr11:107973600-107991800	Weak transcription	Fetal Brain Female	brain

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