Variant report

Variant	rs12290835
Chromosome Location	chr11:73116361-73116362
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	chr11:73112653..73117037-chr11:73375086..73378284,4	MCF-7	breast:
2	chr11:73113711..73116580-chr11:73369932..73372135,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RELT-1	chr11:73116342-73116429	ENSG00000256448.1
2	lnc-RELT-1	chr11:73116342-73116429	ENSG00000256448.1

Variant related genes	Relation type
ENSG00000252732	Chromatin interaction
ENSG00000021300	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1002126	1.00[JPT][hapmap]
rs10898919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11235738	1.00[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];1.00[ASN][1000 genomes]
rs11235740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235746	1.00[JPT][hapmap]
rs11235759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235809	1.00[JPT][hapmap]
rs11820929	1.00[JPT][hapmap]
rs11821094	1.00[JPT][hapmap]
rs11823913	1.00[JPT][hapmap]
rs11823923	1.00[JPT][hapmap]
rs11824614	1.00[JPT][hapmap]
rs11825028	0.89[ASN][1000 genomes]
rs11826896	1.00[JPT][hapmap]
rs11826909	1.00[JPT][hapmap]
rs11828904	1.00[JPT][hapmap]
rs12269884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12275766	1.00[JPT][hapmap]
rs12276892	1.00[JPT][hapmap]
rs12282282	1.00[JPT][hapmap]
rs12282790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12285885	1.00[JPT][hapmap]
rs12288753	1.00[JPT][hapmap]
rs12288934	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12290367	1.00[ASN][1000 genomes]
rs12290623	1.00[JPT][hapmap]
rs12293596	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13328886	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894076	1.00[JPT][hapmap]
rs1938777	1.00[JPT][hapmap]
rs2027761	1.00[JPT][hapmap]
rs2027763	1.00[JPT][hapmap]
rs2298469	1.00[JPT][hapmap]
rs2298807	1.00[JPT][hapmap]
rs3741149	1.00[JPT][hapmap]
rs3825005	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3933402	1.00[JPT][hapmap]
rs56721062	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57181830	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57536508	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57727431	0.81[ASN][1000 genomes]
rs58342890	1.00[EUR][1000 genomes]
rs59809325	1.00[EUR][1000 genomes]
rs59955477	1.00[ASN][1000 genomes]
rs59991976	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60038108	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60123349	1.00[EUR][1000 genomes]
rs60349984	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60674215	1.00[EUR][1000 genomes]
rs61396858	1.00[EUR][1000 genomes]
rs61613696	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6592521	1.00[JPT][hapmap]
rs7101831	1.00[JPT][hapmap]
rs7102197	1.00[JPT][hapmap]
rs7113420	1.00[JPT][hapmap]
rs7114009	1.00[JPT][hapmap]
rs7114376	1.00[JPT][hapmap]
rs7118982	1.00[JPT][hapmap]
rs7123298	1.00[JPT][hapmap]
rs7123985	1.00[JPT][hapmap]
rs7125598	1.00[JPT][hapmap]
rs7125978	1.00[JPT][hapmap]
rs7131383	1.00[JPT][hapmap]
rs7131397	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs725103	1.00[JPT][hapmap]
rs7342205	1.00[JPT][hapmap]
rs7930880	1.00[JPT][hapmap]
rs7934218	1.00[JPT][hapmap]
rs7935948	1.00[JPT][hapmap]
rs7941359	1.00[JPT][hapmap]
rs7944099	1.00[JPT][hapmap]
rs7944346	1.00[JPT][hapmap]
rs7952686	1.00[JPT][hapmap]
rs876480	1.00[JPT][hapmap]
rs880317	1.00[JPT][hapmap]
rs947837	1.00[JPT][hapmap]
rs9888198	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9971494	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:73097200-73117600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:73099600-73119200	Weak transcription	Fetal Lung	lung
8	chr11:73100000-73116600	Weak transcription	Pancreas	Pancrea
9	chr11:73100000-73118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:73100200-73117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:73100600-73118600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:73101000-73116400	Weak transcription	Brain Substantia Nigra	brain
13	chr11:73101200-73124800	Weak transcription	Psoas Muscle	Psoas
14	chr11:73103600-73118400	Weak transcription	Esophagus	oesophagus
15	chr11:73103800-73116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:73104600-73123400	Strong transcription	Fetal Stomach	stomach
17	chr11:73104800-73122600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:73105200-73116400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:73105200-73116800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:73105800-73116600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:73106200-73116400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:73106400-73116600	Weak transcription	Gastric	stomach
23	chr11:73106400-73120200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:73107800-73117600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:73108400-73116400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:73110000-73120000	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:73110200-73116600	Weak transcription	Right Ventricle	heart
28	chr11:73110400-73116600	Weak transcription	NHEK	skin
29	chr11:73110600-73116400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:73110600-73121600	Weak transcription	NHDF-Ad	bronchial
31	chr11:73110600-73123200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:73110800-73116400	Weak transcription	HSMM	muscle
33	chr11:73110800-73123000	Weak transcription	HUVEC	blood vessel
34	chr11:73110800-73123200	Weak transcription	NH-A	brain
35	chr11:73110800-73124000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:73111400-73123200	Strong transcription	Thymus	Thymus
37	chr11:73112200-73117200	Weak transcription	Fetal Brain Male	brain
38	chr11:73112800-73118000	Strong transcription	GM12878-XiMat	blood
39	chr11:73112800-73120000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:73112800-73121200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr11:73112800-73123400	Strong transcription	Brain Germinal Matrix	brain
42	chr11:73113000-73116600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:73113000-73118800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:73113000-73119000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:73113000-73126200	Weak transcription	Small Intestine	intestine
46	chr11:73113200-73116400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:73113400-73117800	Weak transcription	HSMMtube	muscle
48	chr11:73113400-73125000	Weak transcription	Right Atrium	heart
49	chr11:73113600-73116400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:73113600-73118400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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