Variant report

Variant	rs11969089
Chromosome Location	chr6:39172421-39172422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39169873..39175586-chr6:39175633..39178676,8	K562	blood:
2	chr6:39171748..39173462-chr6:39174879..39176528,2	MCF-7	breast:
3	chr6:39167435..39172891-chr6:39233498..39237624,6	MCF-7	breast:
4	chr6:39161548..39165736-chr6:39172380..39175639,5	K562	blood:
5	chr6:39156673..39159411-chr6:39170742..39172943,2	K562	blood:
6	chr6:39172344..39173847-chr6:39177275..39179261,2	K562	blood:
7	chr6:39136896..39139136-chr6:39171989..39173790,2	K562	blood:
8	chr6:39170012..39173010-chr6:39194285..39196889,3	MCF-7	breast:
9	chr6:39168413..39175988-chr6:39191555..39198727,12	K562	blood:
10	chr6:39171917..39173795-chr6:39193843..39195805,2	MCF-7	breast:
11	chr6:39162911..39167327-chr6:39168116..39172779,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10305509	1.00[YRI][hapmap]
rs11961670	1.00[EUR][1000 genomes]
rs11961707	0.83[EUR][1000 genomes]
rs11964657	1.00[EUR][1000 genomes]
rs11965515	1.00[EUR][1000 genomes]
rs11967855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11968074	1.00[EUR][1000 genomes]
rs11968202	1.00[AMR][1000 genomes]
rs59403189	1.00[EUR][1000 genomes]
rs6900508	1.00[YRI][hapmap]
rs6906588	1.00[YRI][hapmap]
rs73420543	1.00[EUR][1000 genomes]
rs7738553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9471038	1.00[EUR][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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39156400-39177200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:39163800-39174000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:39164600-39173400	Enhancers	Stomach Mucosa	stomach
7	chr6:39165400-39172600	Weak transcription	Fetal Stomach	stomach
8	chr6:39166000-39174200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:39166200-39173800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:39166400-39178200	Enhancers	Placenta	Placenta
11	chr6:39167400-39178600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:39167800-39173800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:39168600-39173000	Weak transcription	Fetal Kidney	kidney
14	chr6:39169400-39193600	Enhancers	Liver	Liver
15	chr6:39170000-39172600	Enhancers	Gastric	stomach
16	chr6:39170000-39174600	Enhancers	Colonic Mucosa	Colon
17	chr6:39170000-39179400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:39170200-39174000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:39170400-39176000	Weak transcription	Small Intestine	intestine
20	chr6:39170400-39179200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:39170600-39173800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr6:39170600-39174200	Enhancers	Pancreas	Pancrea
23	chr6:39170800-39173400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:39170800-39175200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:39170800-39179200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:39171000-39172600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:39171000-39172800	Flanking Active TSS	Hela-S3	cervix
28	chr6:39171000-39173400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:39171000-39174000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:39171000-39174200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr6:39171000-39176000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:39171000-39179200	Genic enhancers	K562	blood
33	chr6:39171200-39172600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:39171200-39173400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:39171200-39173400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:39171200-39173400	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:39171200-39174000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr6:39171200-39174000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr6:39171200-39174400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr6:39171200-39174600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:39171400-39172600	Weak transcription	Fetal Lung	lung
42	chr6:39171400-39173400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:39171400-39174000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:39171400-39179200	Enhancers	Esophagus	oesophagus
45	chr6:39171600-39172600	Enhancers	Fetal Muscle Trunk	muscle
46	chr6:39171600-39175000	Genic enhancers	Fetal Thymus	thymus
47	chr6:39171800-39173600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:39172000-39172600	Weak transcription	Ovary	ovary
49	chr6:39172000-39173000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:39172000-39174000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links