Variant report

Variant	rs11172108
Chromosome Location	chr12:39822379-39822380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39814931..39819046-chr12:39820377..39824549,5	K562	blood:
2	chr12:39820768..39822606-chr12:39828400..39830596,2	MCF-7	breast:
3	chr12:39822344..39824626-chr12:39834369..39838046,3	MCF-7	breast:
4	chr12:39804581..39806388-chr12:39821812..39823553,2	K562	blood:
5	chr12:39821875..39824994-chr12:39835535..39837994,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10876868	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10876876	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10876886	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10876972	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877100	0.81[EUR][1000 genomes]
rs11171674	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11171675	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11171676	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11171720	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs11171789	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11171891	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11171901	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs11171923	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs11172081	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172174	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172183	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11172235	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172264	0.81[ASN][1000 genomes]
rs11172282	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172293	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172357	0.84[EUR][1000 genomes]
rs11172386	0.83[EUR][1000 genomes]
rs11172392	0.82[EUR][1000 genomes]
rs11172492	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs11172493	0.81[EUR][1000 genomes]
rs11172526	0.81[EUR][1000 genomes]
rs11172592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11172661	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11830643	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs11836755	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12228767	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs12230604	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12424345	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1512936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1567739	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs1828653	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2388320	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs3736466	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4284427	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs4320988	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs4390378	0.86[EUR][1000 genomes]
rs4492858	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4500523	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4564382	0.81[ASN][1000 genomes]
rs58240943	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58613501	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60900225	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581187	0.84[EUR][1000 genomes]
rs7133376	0.81[YRI][hapmap]
rs7137143	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs73094410	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316073	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs7962283	0.96[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964447	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7965222	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968837	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs7974928	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7979444	0.83[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39785000-39829200	Weak transcription	K562	blood
2	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
3	chr12:39806600-39834200	Weak transcription	Hela-S3	cervix
4	chr12:39808600-39830800	Weak transcription	Fetal Brain Female	brain
5	chr12:39813600-39833400	Weak transcription	Brain Germinal Matrix	brain
6	chr12:39814200-39825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:39814400-39833800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:39816000-39834000	Weak transcription	Left Ventricle	heart
9	chr12:39817400-39824600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:39817400-39824600	Weak transcription	Right Ventricle	heart
11	chr12:39818400-39823200	Weak transcription	Fetal Heart	heart
12	chr12:39819000-39822800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:39819000-39824600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:39820000-39822400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:39820200-39822600	Enhancers	HMEC	breast
16	chr12:39820200-39824000	Enhancers	HepG2	liver
17	chr12:39821000-39823000	Enhancers	NHEK	skin
18	chr12:39821400-39835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:39822000-39823000	Weak transcription	Liver	Liver
20	chr12:39822000-39829800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:39822200-39822400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:39822200-39832200	Weak transcription	A549	lung
23	chr12:39822200-39833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links