Variant report

Variant	rs12907814
Chromosome Location	chr15:78336310-78336311
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78334090..78336952-chr15:78350670..78353482,2	MCF-7	breast:
2	chr15:78329401..78332301-chr15:78334192..78337171,4	K562	blood:
3	chr15:78335660..78338576-chr15:78374188..78376169,2	MCF-7	breast:
4	chr15:78330789..78332749-chr15:78335329..78337205,2	K562	blood:

Variant related genes	Relation type
ENSG00000221476	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1004855	0.83[EUR][1000 genomes]
rs11631578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634607	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638311	0.82[ASN][1000 genomes]
rs11852768	0.98[ASN][1000 genomes]
rs12148365	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594823	0.89[AFR][1000 genomes]
rs12899061	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901812	0.96[ASN][1000 genomes]
rs12907701	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911332	0.81[EUR][1000 genomes]
rs12916362	0.98[ASN][1000 genomes]
rs1348257	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442293	0.95[ASN][1000 genomes]
rs17477813	0.81[AMR][1000 genomes]
rs1837913	0.95[ASN][1000 genomes]
rs2028546	0.82[ASN][1000 genomes]
rs2044099	0.81[ASN][1000 genomes]
rs2867985	0.95[ASN][1000 genomes]
rs2903702	0.97[ASN][1000 genomes]
rs3803380	0.92[ASN][1000 genomes]
rs4886553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886555	0.94[ASN][1000 genomes]
rs4886994	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886996	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886999	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4887000	0.98[ASN][1000 genomes]
rs56317829	0.92[ASN][1000 genomes]
rs57220134	0.95[ASN][1000 genomes]
rs58578288	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62011511	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166819	0.98[ASN][1000 genomes]
rs7170746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173128	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8029562	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030999	0.81[AFR][1000 genomes]
rs9047	0.94[ASN][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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78321200-78343800	Weak transcription	NHEK	skin
11	chr15:78322200-78336600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:78322200-78341000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:78322400-78336600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:78325600-78337800	Genic enhancers	Fetal Thymus	thymus
15	chr15:78327400-78339600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:78327800-78342000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:78328000-78336600	Weak transcription	Fetal Brain Female	brain
19	chr15:78328000-78336800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:78328000-78341800	Weak transcription	Fetal Brain Male	brain
21	chr15:78328400-78339000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:78328400-78342200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78328600-78336400	Weak transcription	NH-A	brain
24	chr15:78328600-78342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:78329000-78342400	Weak transcription	Fetal Heart	heart
26	chr15:78329600-78339000	Weak transcription	Stomach Mucosa	stomach
27	chr15:78330600-78342800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:78331000-78336600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:78331000-78337000	Strong transcription	HSMM	muscle
30	chr15:78331000-78339200	Weak transcription	Brain Angular Gyrus	brain
31	chr15:78331200-78336600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
33	chr15:78331400-78336800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:78331400-78339600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:78331400-78348600	Weak transcription	A549	lung
36	chr15:78331600-78337400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:78331600-78339000	Weak transcription	Right Ventricle	heart
38	chr15:78331600-78339800	Weak transcription	HUVEC	blood vessel
39	chr15:78331600-78348600	Weak transcription	K562	blood
40	chr15:78332000-78336600	Strong transcription	Fetal Intestine Large	intestine
41	chr15:78332000-78336600	Strong transcription	Placenta	Placenta
42	chr15:78332000-78336800	Strong transcription	Fetal Intestine Small	intestine
43	chr15:78332000-78337000	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:78332000-78342200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:78332200-78336400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:78332200-78337000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:78332400-78336600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:78332600-78336600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:78332600-78338600	Strong transcription	Dnd41	blood
50	chr15:78332600-78342000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links