Variant report

Variant	rs28370830
Chromosome Location	chr12:40425604-40425605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10506143	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10506144	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506147	0.87[EUR][1000 genomes]
rs11174631	0.91[AMR][1000 genomes]
rs11174697	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175186	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175593	0.87[EUR][1000 genomes]
rs11564107	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564108	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11564187	0.87[EUR][1000 genomes]
rs11564199	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564212	0.87[EUR][1000 genomes]
rs11564216	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564218	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12422544	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12424040	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12424294	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12425630	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12426378	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426643	0.81[AMR][1000 genomes]
rs12427022	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1388585	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1388597	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17442924	0.86[EUR][1000 genomes]
rs17443078	0.86[EUR][1000 genomes]
rs17443178	0.80[EUR][1000 genomes]
rs17443185	0.86[EUR][1000 genomes]
rs17443206	0.86[EUR][1000 genomes]
rs17458549	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17458808	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17461387	0.81[AMR][1000 genomes]
rs17461575	0.87[EUR][1000 genomes]
rs17465610	0.87[EUR][1000 genomes]
rs17483919	0.81[AMR][1000 genomes]
rs17484003	0.93[EUR][1000 genomes]
rs2638223	0.86[EUR][1000 genomes]
rs2708460	0.86[EUR][1000 genomes]
rs28365169	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28365173	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28365669	0.84[AMR][1000 genomes]
rs28365689	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28370637	0.89[AMR][1000 genomes]
rs28370649	0.93[EUR][1000 genomes]
rs28370650	0.93[EUR][1000 genomes]
rs28370664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767961	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4767965	0.87[EUR][1000 genomes]
rs4768206	0.91[AMR][1000 genomes]
rs4768213	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729215	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	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:37 , 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	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
5	chr12:40406600-40425800	Weak transcription	Liver	Liver
6	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
11	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
12	chr12:40415000-40426000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:40416600-40441800	Weak transcription	Ovary	ovary
14	chr12:40417000-40426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
17	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
18	chr12:40420800-40426000	Weak transcription	Fetal Kidney	kidney
19	chr12:40421600-40427000	Weak transcription	Brain Anterior Caudate	brain
20	chr12:40421600-40428000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
22	chr12:40421800-40427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:40423400-40426000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:40425200-40428000	Enhancers	Fetal Intestine Small	intestine
25	chr12:40425200-40429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:40425400-40425800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:40425400-40426600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:40425400-40428400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr12:40425400-40429200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr12:40425600-40425800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr12:40425600-40425800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr12:40425600-40426200	Enhancers	Stomach Mucosa	stomach
33	chr12:40425600-40426400	Enhancers	Fetal Intestine Large	intestine
34	chr12:40425600-40426800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr12:40425600-40427400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:40425600-40429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr12:40425600-40429800	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links