Variant report

Variant	rs12908199
Chromosome Location	chr15:73371822-73371823
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73304946..73307703-chr15:73371180..73373676,2	MCF-7	breast:
2	chr15:73356525..73360663-chr15:73369090..73372368,3	MCF-7	breast:
3	chr15:73075161..73076721-chr15:73370865..73372957,2	K562	blood:
4	chr15:73074981..73077571-chr15:73371548..73374920,3	MCF-7	breast:
5	chr15:73343238..73345497-chr15:73369477..73372153,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000159322	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11629919	0.83[AMR][1000 genomes]
rs11630441	0.86[AMR][1000 genomes]
rs11630460	1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630572	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632354	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632433	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11637722	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856233	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857768	0.85[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12902056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903656	0.81[EUR][1000 genomes]
rs12909626	0.87[CEU][hapmap]
rs12912599	0.85[EUR][1000 genomes]
rs12913381	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12914663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34160980	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34182754	0.90[AMR][1000 genomes]
rs34291790	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34326722	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34355572	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427117	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34649871	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082203	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35133756	0.90[AMR][1000 genomes]
rs35660974	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35767004	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35768298	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36045491	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4625692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs66473967	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68000913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68139669	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71397276	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71397277	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72741411	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741417	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72741432	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7495433	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024434	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs8029474	0.83[AMR][1000 genomes]
rs8037213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039439	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8039533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73361000-73372400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73365000-73374000	Enhancers	Brain Angular Gyrus	brain
3	chr15:73368200-73375600	Enhancers	Brain Substantia Nigra	brain
4	chr15:73368200-73381000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:73368400-73373200	Enhancers	Brain Anterior Caudate	brain
6	chr15:73368600-73375200	Weak transcription	Aorta	Aorta
7	chr15:73369200-73374600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:73369600-73374200	Enhancers	Brain Hippocampus Middle	brain
9	chr15:73369600-73374400	Enhancers	Brain Cingulate Gyrus	brain
10	chr15:73370000-73372200	Enhancers	Duodenum Mucosa	Duodenum
11	chr15:73370000-73373800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr15:73370200-73372000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr15:73370200-73375600	Enhancers	Stomach Mucosa	stomach
14	chr15:73370600-73373800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr15:73370800-73372200	Enhancers	Fetal Intestine Small	intestine
16	chr15:73370800-73372400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:73370800-73372600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:73370800-73372600	Enhancers	Fetal Lung	lung
19	chr15:73371000-73373000	Weak transcription	Right Atrium	heart
20	chr15:73371000-73373200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr15:73371000-73375200	Weak transcription	Gastric	stomach
22	chr15:73371000-73376600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:73371200-73372600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:73371200-73372600	Weak transcription	Psoas Muscle	Psoas
25	chr15:73371200-73372800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:73371200-73376800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:73371200-73388600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:73371200-73397000	Weak transcription	Pancreas	Pancrea
29	chr15:73371400-73372000	Enhancers	Liver	Liver
30	chr15:73371400-73375200	Weak transcription	A549	lung
31	chr15:73371600-73372000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:73371600-73372000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:73371600-73372400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:73371600-73372400	Weak transcription	Small Intestine	intestine
35	chr15:73371600-73372800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:73371600-73372800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:73371600-73372800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:73371600-73373800	Weak transcription	Fetal Intestine Large	intestine
39	chr15:73371600-73374000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:73371600-73377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:73371600-73393800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:73371800-73372200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:73371800-73372200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:73371800-73372200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:73371800-73375000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:73371800-73375200	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links