Variant report

Variant	rs13087169
Chromosome Location	chr3:140998214-140998215
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140911231..140911800-chr3:140998106..140998618,2	MCF-7	breast:
2	chr3:140995854..140998314-chr3:141085270..141088004,2	K562	blood:
3	chr3:140948408..140951597-chr3:140996026..140999585,4	MCF-7	breast:
4	chr3:140998105..140999651-chr3:141029649..141032061,2	K562	blood:
5	chr3:140950179..140950829-chr3:140997848..140998729,3	MCF-7	breast:
6	chr3:140998144..141000121-chr3:141003394..141004994,2	K562	blood:
7	chr3:140949711..140951021-chr3:140997855..140998457,3	K562	blood:
8	chr3:140945385..140947466-chr3:140997029..140999166,2	MCF-7	breast:
9	chr3:140994584..140997206-chr3:140998045..141000417,2	K562	blood:
10	chr3:140996819..140999221-chr3:141004642..141007259,2	MCF-7	breast:
11	chr3:140946905..140947767-chr3:140997819..140998807,6	MCF-7	breast:
12	chr3:140997890..141000660-chr3:141000973..141003203,2	K562	blood:
13	chr3:140992520..140994223-chr3:140997053..141000025,2	K562	blood:
14	chr3:140998151..140999834-chr3:141030561..141032150,2	K562	blood:
15	chr3:140910860..140911731-chr3:140997895..140998782,2	K562	blood:
16	chr3:140991760..140994020-chr3:140996635..140998553,2	K562	blood:
17	chr3:140995281..140996903-chr3:140996967..140998531,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10935425	0.82[CEU][hapmap]
rs10935427	0.81[CEU][hapmap];0.95[GIH][hapmap]
rs11921252	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs13088065	0.86[EUR][1000 genomes]
rs1567559	0.81[CEU][hapmap]
rs1877223	0.92[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4683399	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs6772725	0.81[AFR][1000 genomes]
rs6775902	0.82[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs6786821	0.96[CEU][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9819731	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13087169	TRPC1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
4	chr3:140979000-141000800	Weak transcription	Fetal Kidney	kidney
5	chr3:140979000-141013200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:140980800-141005600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:140981000-140998400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:140981200-141013200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:140981200-141013400	Weak transcription	Colonic Mucosa	Colon
10	chr3:140981400-141001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:140983600-141021600	Weak transcription	Esophagus	oesophagus
12	chr3:140984200-141000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:140984800-141006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:140986200-141000800	Weak transcription	Fetal Lung	lung
15	chr3:140988200-141022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:140988400-141001800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:140990800-140998600	Weak transcription	Gastric	stomach
18	chr3:140991000-140999600	Weak transcription	Pancreas	Pancrea
19	chr3:140993200-141014200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:140993400-140998400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:140993600-141004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:140993800-140998400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:140993800-140998600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:140993800-140999600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:140994000-141006000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:140994200-140999400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:140994400-141000200	Weak transcription	Ovary	ovary
28	chr3:140994400-141005600	Weak transcription	GM12878-XiMat	blood
29	chr3:140994400-141009000	Strong transcription	Dnd41	blood
30	chr3:140994600-141006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:140994600-141012400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:140994600-141013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:140995200-141007000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:140995400-141009000	Weak transcription	HepG2	liver
35	chr3:140995600-140998400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:140996000-141012400	Strong transcription	Thymus	Thymus
37	chr3:140996200-140998400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:140996200-141012400	Strong transcription	Primary T cells from cord blood	blood
39	chr3:140996400-140998600	Strong transcription	Fetal Stomach	stomach
40	chr3:140996400-140998600	Enhancers	Lung	lung
41	chr3:140996400-140999600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:140996400-141000400	Enhancers	Fetal Heart	heart
43	chr3:140996400-141004600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:140996400-141012800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:140996600-141002000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:140996800-140998600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:140996800-140999800	Strong transcription	Fetal Intestine Large	intestine
48	chr3:140997200-140999400	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr3:140997200-141006200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:140997200-141013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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