Variant report

Variant	rs11634607
Chromosome Location	chr15:78334655-78334656
allele	C/T
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	chr15:78333663..78335514-chr15:78341566..78343908,2	K562	blood:
3	chr15:78329401..78332301-chr15:78334192..78337171,4	K562	blood:
4	chr15:78332545..78335150-chr15:78348925..78351809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221476	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1004855	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10519181	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs11072716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638311	0.83[ASN][1000 genomes]
rs11852768	0.99[ASN][1000 genomes]
rs12148365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12591418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594823	1.00[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs12899061	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs12907701	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs12916362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1348257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs17477813	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs1837913	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs2028546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2044099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs2867985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2903702	0.98[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs4886553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886555	0.96[ASN][1000 genomes]
rs4886994	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4886996	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56317829	0.93[ASN][1000 genomes]
rs57220134	0.97[ASN][1000 genomes]
rs58578288	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62011511	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166819	0.99[ASN][1000 genomes]
rs7170746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs7181594	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029562	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs8030999	0.94[ASW][hapmap];0.84[LWK][hapmap];0.80[AFR][1000 genomes]
rs9047	0.96[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11634607	HEXA	cis	parietal	SCAN
rs11634607	ISL2	cis	parietal	SCAN
rs11634607	CLK3	cis	cerebellum	SCAN

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	chr15:78328000-78335400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:78328000-78336600	Weak transcription	Fetal Brain Female	brain
20	chr15:78328000-78336800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:78328000-78341800	Weak transcription	Fetal Brain Male	brain
22	chr15:78328400-78334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:78328400-78339000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:78328400-78342200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:78328600-78336400	Weak transcription	NH-A	brain
26	chr15:78328600-78342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:78329000-78342400	Weak transcription	Fetal Heart	heart
28	chr15:78329400-78336200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:78329600-78339000	Weak transcription	Stomach Mucosa	stomach
30	chr15:78330600-78342800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:78331000-78336200	Strong transcription	Fetal Stomach	stomach
32	chr15:78331000-78336600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:78331000-78337000	Strong transcription	HSMM	muscle
34	chr15:78331000-78339200	Weak transcription	Brain Angular Gyrus	brain
35	chr15:78331200-78336600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
37	chr15:78331400-78336800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:78331400-78339600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:78331400-78348600	Weak transcription	A549	lung
40	chr15:78331600-78337400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:78331600-78339000	Weak transcription	Right Ventricle	heart
42	chr15:78331600-78339800	Weak transcription	HUVEC	blood vessel
43	chr15:78331600-78348600	Weak transcription	K562	blood
44	chr15:78332000-78334800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:78332000-78336600	Strong transcription	Fetal Intestine Large	intestine
46	chr15:78332000-78336600	Strong transcription	Placenta	Placenta
47	chr15:78332000-78336800	Strong transcription	Fetal Intestine Small	intestine
48	chr15:78332000-78337000	Strong transcription	Fetal Muscle Leg	muscle
49	chr15:78332000-78342200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:78332200-78335600	Weak transcription	Small Intestine	intestine

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