Variant report

Variant	rs12575005
Chromosome Location	chr11:35254323-35254324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:35253589..35256594-chr11:35257104..35259626,3	MCF-7	breast:
2	chr11:35251288..35252930-chr11:35253929..35256719,2	K562	blood:
3	chr11:35253382..35256689-chr11:35262779..35266276,3	K562	blood:
4	chr11:35253382..35256369-chr11:35263187..35265388,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC1A2-4	chr11:35254171-35254874	NONHSAT018787

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10444271	1.00[YRI][hapmap]
rs10488813	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10836347	0.86[CEU][hapmap];0.96[EUR][1000 genomes]
rs10836349	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836352	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836353	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836358	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033031	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs11033034	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033039	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033041	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11033071	1.00[YRI][hapmap]
rs12360706	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12364027	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570216	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16927292	1.00[YRI][hapmap]
rs3794097	1.00[YRI][hapmap]
rs3812778	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829280	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3891872	1.00[YRI][hapmap]
rs4083481	1.00[YRI][hapmap]
rs41525047	1.00[YRI][hapmap]
rs4503504	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4508184	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55715534	0.81[EUR][1000 genomes]
rs56193087	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67384276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7104662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7122374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638195	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72916162	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv897216	chr11:35241989-35255821	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv897217	chr11:35241989-35257316	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv897218	chr11:35241989-35261374	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv897219	chr11:35242907-35257316	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv897220	chr11:35242907-35261374	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv897221	chr11:35242907-35265444	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv897222	chr11:35244044-35261374	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35233400-35259600	Weak transcription	Liver	Liver
2	chr11:35236200-35254400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:35236800-35259600	Weak transcription	Psoas Muscle	Psoas
4	chr11:35237000-35254600	Strong transcription	HSMM	muscle
5	chr11:35237000-35259600	Weak transcription	HUVEC	blood vessel
6	chr11:35239200-35257600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:35239800-35254600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr11:35239800-35254600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:35239800-35255000	Strong transcription	Primary T cells from cord blood	blood
10	chr11:35240600-35254400	Strong transcription	NH-A	brain
11	chr11:35240800-35254600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:35241200-35259600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:35243200-35254400	Strong transcription	A549	lung
14	chr11:35243600-35258200	Weak transcription	GM12878-XiMat	blood
15	chr11:35245400-35259600	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:35245800-35255400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:35245800-35256600	Weak transcription	Small Intestine	intestine
18	chr11:35246600-35254800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:35247000-35258000	Weak transcription	Colonic Mucosa	Colon
20	chr11:35247000-35263200	Weak transcription	HSMMtube	muscle
21	chr11:35247200-35257600	Weak transcription	Thymus	Thymus
22	chr11:35249400-35254800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:35249800-35254600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:35250600-35254600	Strong transcription	Primary B cells from cord blood	blood
25	chr11:35251000-35254600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:35251000-35256000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:35251400-35259400	Weak transcription	Left Ventricle	heart
28	chr11:35251400-35259800	Weak transcription	Gastric	stomach
29	chr11:35252000-35257800	Weak transcription	Pancreas	Pancrea
30	chr11:35252200-35257400	Weak transcription	Stomach Mucosa	stomach
31	chr11:35252200-35258000	Weak transcription	Placenta	Placenta
32	chr11:35252200-35259400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:35252400-35256600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:35252400-35258600	Weak transcription	Fetal Lung	lung
35	chr11:35252400-35259400	Weak transcription	Lung	lung
36	chr11:35252600-35256600	Weak transcription	Esophagus	oesophagus
37	chr11:35252600-35257400	Weak transcription	Fetal Thymus	thymus
38	chr11:35252800-35254600	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:35253000-35254400	Weak transcription	Aorta	Aorta
40	chr11:35253000-35254400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:35253000-35254600	Weak transcription	Fetal Stomach	stomach
42	chr11:35253000-35255800	Weak transcription	Dnd41	blood
43	chr11:35253000-35256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:35253000-35256800	Weak transcription	Hela-S3	cervix
45	chr11:35253000-35257400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:35253000-35258000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:35253000-35259400	Weak transcription	Adipose Nuclei	Adipose
48	chr11:35253000-35260400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:35253200-35254800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:35253200-35255200	Weak transcription	Rectal Smooth Muscle	rectum

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