Variant report

Variant	rs11709900
Chromosome Location	chr3:142317349-142317350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
2	chr3:142316986..142319598-chr3:142354070..142355822,2	MCF-7	breast:
3	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242390	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11707731	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13075800	0.87[EUR][1000 genomes]
rs13091637	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16852464	0.87[EUR][1000 genomes]
rs34660854	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35238606	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67594010	0.87[EUR][1000 genomes]
rs68065420	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142314200-142317800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:142314400-142317400	Active TSS	Colonic Mucosa	Colon
3	chr3:142314400-142317400	Active TSS	Fetal Kidney	kidney
4	chr3:142314400-142317600	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:142314400-142317800	Active TSS	Duodenum Mucosa	Duodenum
6	chr3:142314600-142317600	Active TSS	Stomach Mucosa	stomach
7	chr3:142315600-142317400	Flanking Active TSS	Dnd41	blood
8	chr3:142315600-142319200	Weak transcription	Gastric	stomach
9	chr3:142315800-142318000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:142315800-142320400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:142315800-142324400	Weak transcription	Lung	lung
12	chr3:142316000-142317400	Enhancers	Fetal Thymus	thymus
13	chr3:142316000-142319800	Weak transcription	NH-A	brain
14	chr3:142316000-142321000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:142316000-142321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:142316200-142317400	Enhancers	Liver	Liver
17	chr3:142316200-142317400	Enhancers	Hela-S3	cervix
18	chr3:142316200-142318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:142316200-142331000	Weak transcription	Small Intestine	intestine
20	chr3:142316400-142317400	Enhancers	Esophagus	oesophagus
21	chr3:142316400-142317400	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr3:142316600-142317400	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:142316800-142317400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:142316800-142317800	Enhancers	Pancreas	Pancrea
25	chr3:142317000-142317400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:142317000-142317400	Enhancers	HepG2	liver
27	chr3:142317000-142321000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:142317000-142327600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:142317200-142317400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:142317200-142317400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:142317200-142317400	Flanking Active TSS	A549	lung
32	chr3:142317200-142317400	Enhancers	K562	blood
33	chr3:142317200-142317400	Enhancers	NHEK	skin
34	chr3:142317200-142317600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:142317200-142317800	Enhancers	Fetal Intestine Large	intestine
36	chr3:142317200-142321800	Weak transcription	Thymus	Thymus
37	chr3:142317200-142337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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