Variant report

Variant	rs11072463
Chromosome Location	chr15:74303349-74303350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74302863..74303504-chr15:74316793..74317518,2	MCF-7	breast:
2	chr15:74283960..74290618-chr15:74296413..74304371,10	MCF-7	breast:
3	chr15:74303068..74303808-chr15:74316250..74317180,2	MCF-7	breast:
4	chr15:74301606..74304928-chr15:74311289..74313632,4	MCF-7	breast:
5	chr15:74277595..74279838-chr15:74301921..74304643,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140464	Chromatin interaction
ENSG00000067221	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10162627	0.81[CEU][hapmap];0.95[MEX][hapmap]
rs1052242	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1052246	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10851866	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10851867	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851868	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10851869	0.95[MKK][hapmap];0.83[YRI][hapmap]
rs11072458	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11072461	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072462	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072464	0.81[CEU][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs11072469	0.82[CEU][hapmap]
rs11633735	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635930	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636016	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636065	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11636150	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11854321	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857498	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442211	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs12592370	0.83[MEX][hapmap]
rs12593528	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899085	0.82[AMR][1000 genomes]
rs12901603	0.81[AMR][1000 genomes]
rs12902857	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12902945	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12904213	0.80[AMR][1000 genomes]
rs12908748	0.82[AMR][1000 genomes]
rs12910581	0.89[AMR][1000 genomes]
rs12911807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911984	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550435	0.87[MKK][hapmap]
rs2165242	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277599	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2304715	0.81[AMR][1000 genomes]
rs2304716	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304717	0.83[MEX][hapmap]
rs2304718	0.83[MEX][hapmap]
rs2415206	0.85[AMR][1000 genomes]
rs3784561	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784562	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4287518	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547288	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4886820	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4886844	0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs4886845	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4886846	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56194867	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183908	0.85[ASN][1000 genomes]
rs734854	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743580	0.90[ASN][1000 genomes]
rs752004	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MKK][hapmap];0.90[ASN][1000 genomes]
rs8027327	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8027447	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8027774	0.84[CEU][hapmap]
rs8028557	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039276	0.81[AMR][1000 genomes]
rs8039404	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043489	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs9479	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11072463	LARP6	cis	parietal	SCAN
rs11072463	CYP11A1	cis	cerebellum	SCAN
rs11072463	BBS4	cis	parietal	SCAN
rs11072463	STOML1	cis	parietal	SCAN
rs11072463	ADPGK	cis	parietal	SCAN
rs11072463	KIAA1462	trans	parietal	SCAN
rs11072463	STOML1	cis	cerebellum	SCAN
rs11072463	DMBX1	trans	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74303800	Weak transcription	Brain Angular Gyrus	brain
2	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
3	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:74290000-74303400	Weak transcription	Fetal Kidney	kidney
5	chr15:74290000-74314800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:74291000-74311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:74291000-74314800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:74291000-74315000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:74291000-74315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:74291800-74314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:74292000-74315200	Weak transcription	Fetal Brain Female	brain
12	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
13	chr15:74293400-74303600	Weak transcription	NH-A	brain
14	chr15:74296600-74315200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:74296800-74315200	Weak transcription	Brain Germinal Matrix	brain
16	chr15:74297000-74315200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:74297000-74315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:74298000-74303800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:74298000-74304200	Enhancers	Right Atrium	heart
20	chr15:74298200-74311200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:74299000-74304200	Enhancers	Right Ventricle	heart
22	chr15:74299200-74303600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:74299200-74315400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:74299400-74304000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr15:74299400-74304600	Enhancers	Left Ventricle	heart
26	chr15:74299400-74315400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:74299600-74308200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr15:74299800-74303400	Weak transcription	Fetal Intestine Large	intestine
29	chr15:74299800-74303800	Genic enhancers	Fetal Muscle Leg	muscle
30	chr15:74300000-74314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:74300400-74303400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:74300400-74303800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:74300400-74304200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:74300400-74307000	Weak transcription	HSMMtube	muscle
35	chr15:74300400-74315800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:74300600-74303400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:74300600-74303400	Weak transcription	Aorta	Aorta
38	chr15:74300600-74303400	Weak transcription	Brain Anterior Caudate	brain
39	chr15:74300600-74303400	Enhancers	Stomach Mucosa	stomach
40	chr15:74300600-74303400	Enhancers	HUVEC	blood vessel
41	chr15:74300600-74303400	Weak transcription	K562	blood
42	chr15:74300600-74307600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:74300600-74307800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:74300600-74315200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:74300800-74303400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr15:74300800-74303600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:74300800-74303800	Enhancers	Colon Smooth Muscle	Colon
48	chr15:74300800-74304400	Enhancers	Spleen	Spleen
49	chr15:74300800-74305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:74300800-74306400	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links