Variant report

Variant	rs1071695
Chromosome Location	chr11:35201842-35201843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:35197745-35203204	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:35201725-35202077	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:35201768-35202160	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:35197908-35203212	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:35197880-35203195	U87	brain:	n/a	n/a
6	POLR2A	chr11:35197784-35203201	U87	brain:	n/a	n/a
7	POLR2A	chr11:35198885-35203035	GM12892	blood:	n/a	n/a
8	POLR2A	chr11:35201688-35202114	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:35201609-35203175	GM12892	blood:	n/a	n/a
10	POLR2A	chr11:35201587-35203224	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:35198835-35203167	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:35201792-35202266	GM12891	blood:	n/a	n/a
13	POU5F1	chr11:35201793-35202287	H1-hESC	embryonic stem cell:	n/a	chr11:35202045-35202059 chr11:35202045-35202059 chr11:35202045-35202053 chr11:35202045-35202059 chr11:35202044-35202058
14	POLR2A	chr11:35199668-35202263	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:35198801-35203213	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35199491..35202638-chr11:35207456..35210593,3	MCF-7	breast:

Variant related genes	Relation type
CD44	TF binding region
ENSG00000026508	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11033013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1570483	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16926995	0.80[CHB][hapmap]
rs17445923	0.80[CHB][hapmap]
rs17445972	0.80[CHB][hapmap]
rs34443928	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35605320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35861024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61881656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61881658	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6484768	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs71480068	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952493	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	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
10	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
11	esv3693078	chr11:35179651-35217745	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1071695	LMO2	cis	parietal	SCAN
rs1071695	RAG1	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35189400-35213800	Weak transcription	Right Ventricle	heart
2	chr11:35189400-35218800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:35189600-35204800	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:35190200-35204400	Weak transcription	Brain Substantia Nigra	brain
5	chr11:35192200-35202000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:35195000-35211200	Weak transcription	Gastric	stomach
7	chr11:35195800-35213600	Weak transcription	Liver	Liver
8	chr11:35196000-35212200	Weak transcription	Fetal Intestine Small	intestine
9	chr11:35197000-35211600	Weak transcription	HUVEC	blood vessel
10	chr11:35197600-35202600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:35198000-35202600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:35198000-35202600	Strong transcription	Fetal Stomach	stomach
13	chr11:35198000-35202800	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr11:35198000-35202800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:35198000-35203200	Genic enhancers	Osteobl	bone
16	chr11:35198000-35204400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:35198000-35204400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr11:35198000-35208400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:35198000-35208600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr11:35198000-35223600	Strong transcription	Dnd41	blood
21	chr11:35198000-35232800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:35198200-35202000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr11:35198200-35202000	Strong transcription	Spleen	Spleen
24	chr11:35198200-35202600	Genic enhancers	HMEC	breast
25	chr11:35198200-35203000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:35198200-35203000	Genic enhancers	NH-A	brain
27	chr11:35198200-35204600	Genic enhancers	NHLF	lung
28	chr11:35198200-35210000	Genic enhancers	NHDF-Ad	bronchial
29	chr11:35198200-35219800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:35198400-35202600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:35198400-35202800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:35198400-35213000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:35198800-35202400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:35198800-35202600	Genic enhancers	Fetal Muscle Leg	muscle
35	chr11:35198800-35203000	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr11:35198800-35204400	Genic enhancers	NHEK	skin
37	chr11:35199000-35202200	Genic enhancers	Hela-S3	cervix
38	chr11:35199000-35202600	Genic enhancers	Rectal Mucosa Donor 29	rectum
39	chr11:35199000-35204600	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr11:35199200-35202000	Genic enhancers	Adipose Nuclei	Adipose
41	chr11:35199200-35202600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:35199200-35203200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr11:35199400-35202000	Enhancers	Colonic Mucosa	Colon
44	chr11:35199400-35203000	Genic enhancers	Colon Smooth Muscle	Colon
45	chr11:35199400-35204000	Genic enhancers	Primary B cells from cord blood	blood
46	chr11:35199400-35207200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:35199400-35211600	Weak transcription	Fetal Intestine Large	intestine
48	chr11:35199600-35202200	Genic enhancers	Lung	lung
49	chr11:35199600-35202200	Genic enhancers	A549	lung
50	chr11:35199600-35202400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links