Variant report

Variant	rs10877971
Chromosome Location	chr12:40426177-40426178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40425499..40426450-chr12:40706505..40707111,2	MCF-7	breast:
2	chr12:40424834..40427522-chr12:40498279..40501048,3	MCF-7	breast:
3	chr12:40425798..40426494-chr12:40501097..40501912,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151229	Chromatin interaction
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10082797	0.82[CHB][hapmap]
rs10784340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878036	0.81[CHB][hapmap]
rs10878123	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11174603	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11174831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175102	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175103	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs11175260	0.86[EUR][1000 genomes]
rs11175371	1.00[YRI][hapmap]
rs11175401	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11175422	1.00[CEU][hapmap]
rs12372213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12581285	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1472117	1.00[YRI][hapmap]
rs1491924	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17442157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17458156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17458613	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs17518546	0.86[EUR][1000 genomes]
rs2708437	1.00[YRI][hapmap]
rs2708438	1.00[YRI][hapmap]
rs28365172	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28365179	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28365683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370683	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7971218	0.82[CHB][hapmap]
rs949640	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
6	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
7	chr12:40416600-40441800	Weak transcription	Ovary	ovary
8	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
10	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
11	chr12:40421600-40427000	Weak transcription	Brain Anterior Caudate	brain
12	chr12:40421600-40428000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
14	chr12:40421800-40427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:40425200-40428000	Enhancers	Fetal Intestine Small	intestine
16	chr12:40425200-40429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:40425400-40426600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:40425400-40428400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:40425400-40429200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:40425600-40426200	Enhancers	Stomach Mucosa	stomach
21	chr12:40425600-40426400	Enhancers	Fetal Intestine Large	intestine
22	chr12:40425600-40426800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:40425600-40427400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:40425600-40429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:40425600-40429800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:40425800-40426200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:40425800-40426200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:40425800-40426400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:40425800-40426400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr12:40426000-40426200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:40426000-40426200	Active TSS	Duodenum Mucosa	Duodenum
32	chr12:40426000-40426400	Flanking Active TSS	Liver	Liver
33	chr12:40426000-40426600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr12:40426000-40426600	Enhancers	Fetal Kidney	kidney
35	chr12:40426000-40426800	Enhancers	Fetal Lung	lung
36	chr12:40426000-40427000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr12:40426000-40427200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr12:40426000-40427400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:40426000-40427400	Enhancers	Pancreas	Pancrea
40	chr12:40426000-40428200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr12:40426000-40428800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr12:40426000-40429000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links