Variant report

Variant	rs13357640
Chromosome Location	chr5:41795421-41795422
allele	A/G
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	chr5:41795237-41795513	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr5:41794279-41795454	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:41795218-41795532	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:41795358-41795460	ProgFib	skin:	n/a	n/a
5	JUND	chr5:41794052-41795690	SK-N-SH	brain:	n/a	chr5:41794722-41794733
6	EP300	chr5:41792262-41795616	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
OXCT1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10037152	0.83[AFR][1000 genomes]
rs10038717	1.00[AFR][1000 genomes]
rs10039091	0.95[AFR][1000 genomes]
rs10042050	0.87[AFR][1000 genomes]
rs10045224	0.91[AFR][1000 genomes]
rs10064781	0.86[AFR][1000 genomes]
rs10072903	0.95[AFR][1000 genomes]
rs10079775	0.91[AFR][1000 genomes]
rs10080034	0.91[AFR][1000 genomes]
rs10214013	1.00[AFR][1000 genomes]
rs10473254	0.91[AFR][1000 genomes]
rs13354429	0.95[AFR][1000 genomes]
rs13358155	0.95[AFR][1000 genomes]
rs28429157	0.87[AFR][1000 genomes]
rs28588578	1.00[AFR][1000 genomes]
rs28661292	0.87[AFR][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	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41731400-41800400	Weak transcription	Small Intestine	intestine
2	chr5:41735800-41800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:41739400-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:41749200-41797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:41756200-41813800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:41759800-41800400	Weak transcription	Esophagus	oesophagus
7	chr5:41761200-41798400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:41761600-41804600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:41762000-41799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:41776000-41798200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:41778200-41838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:41780000-41800200	Weak transcription	Fetal Intestine Large	intestine
13	chr5:41784800-41796200	Weak transcription	K562	blood
14	chr5:41785800-41800000	Weak transcription	Fetal Brain Male	brain
15	chr5:41788600-41800000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:41789600-41808200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:41790200-41801400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:41790200-41801600	Strong transcription	Primary T cells from cord blood	blood
19	chr5:41790400-41814000	Weak transcription	Psoas Muscle	Psoas
20	chr5:41791000-41801200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:41791600-41807600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr5:41792200-41795600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:41792200-41801000	Strong transcription	Primary B cells from cord blood	blood
24	chr5:41792200-41801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:41792400-41795600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:41792400-41795600	Enhancers	Fetal Stomach	stomach
27	chr5:41792400-41795800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:41792400-41796800	Strong transcription	Dnd41	blood
29	chr5:41792400-41799000	Strong transcription	Fetal Thymus	thymus
30	chr5:41792600-41795800	Enhancers	Fetal Lung	lung
31	chr5:41792600-41798800	Strong transcription	GM12878-XiMat	blood
32	chr5:41792600-41800400	Weak transcription	Gastric	stomach
33	chr5:41792800-41796600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:41792800-41796600	Enhancers	NHDF-Ad	bronchial
35	chr5:41793000-41795600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:41793000-41796600	Enhancers	NHLF	lung
37	chr5:41793000-41800200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:41793200-41796000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:41793200-41796600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:41793200-41796600	Enhancers	Fetal Heart	heart
41	chr5:41793200-41797200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:41793200-41797200	Enhancers	NHEK	skin
43	chr5:41793200-41797200	Enhancers	Osteobl	bone
44	chr5:41793400-41795600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:41793400-41800400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:41793400-41801200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:41793400-41810400	Weak transcription	Spleen	Spleen
48	chr5:41793600-41796600	Enhancers	HMEC	breast
49	chr5:41793800-41795600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:41793800-41795600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links