Variant report

Variant	rs7931630
Chromosome Location	chr11:18547332-18547333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18546372..18549758-chr11:18653531..18658575,7	K562	blood:
2	chr11:18530137..18532670-chr11:18545448..18547562,2	K562	blood:
3	chr11:18546581..18551368-chr11:18654825..18657467,6	K562	blood:
4	chr11:18342189..18343915-chr11:18546820..18548379,2	MCF-7	breast:
5	chr11:18341846..18344494-chr11:18547115..18549354,2	MCF-7	breast:
6	chr11:18547238..18549661-chr11:18600782..18603302,3	MCF-7	breast:
7	chr11:18414795..18417618-chr11:18546727..18549809,4	MCF-7	breast:
8	chr11:18430626..18432747-chr11:18545645..18547445,2	K562	blood:
9	chr11:18546303..18549278-chr11:18609985..18612598,2	K562	blood:
10	chr11:18343253..18347316-chr11:18546908..18550670,5	K562	blood:
11	chr11:18533507..18535848-chr11:18546408..18548301,3	K562	blood:
12	chr11:18531181..18534158-chr11:18547173..18549352,2	MCF-7	breast:
13	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256361	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000256588	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10500836	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10741747	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10766483	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832939	0.80[YRI][hapmap]
rs10832940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832941	0.85[JPT][hapmap]
rs11024690	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024699	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024717	0.86[JPT][hapmap]
rs12224694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12225037	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12419063	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12574808	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577346	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935538	0.80[YRI][hapmap]
rs1857907	0.93[JPT][hapmap]
rs2132302	0.93[JPT][hapmap]
rs2658552	0.86[JPT][hapmap]
rs2658564	0.85[JPT][hapmap]
rs34457574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3925781	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4298881	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4623881	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756952	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56333121	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6486430	0.86[JPT][hapmap]
rs6486431	0.80[YRI][hapmap]
rs6486434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7105889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7107057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119085	1.00[JPT][hapmap]
rs7129164	0.93[JPT][hapmap]
rs7928872	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs7934817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7951508	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7952284	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7931630	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs7931630	TSG101	cis	Lymphoblastoid	GTEx
rs7931630	TSG101	cis	multi-tissue	Pritchard
rs7931630	LDHC	cis	Thyroid	GTEx
rs7931630	TSG101	cis	Muscle Skeletal	GTEx
rs7931630	TSG101	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:18523800-18547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:18524200-18547400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:18532800-18547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:18535400-18547800	Weak transcription	Esophagus	oesophagus
6	chr11:18535600-18547600	Weak transcription	Aorta	Aorta
7	chr11:18535800-18547400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:18535800-18547800	Weak transcription	Lung	lung
9	chr11:18536800-18547400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:18537200-18547400	Weak transcription	Colonic Mucosa	Colon
11	chr11:18537400-18547400	Weak transcription	Brain Anterior Caudate	brain
12	chr11:18537400-18547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:18537800-18547400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:18537800-18547400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:18540400-18547400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr11:18543600-18547400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:18544200-18547400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:18544400-18547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:18544400-18547400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:18544800-18547400	Weak transcription	Right Atrium	heart
21	chr11:18544800-18547600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:18544800-18547800	Weak transcription	Left Ventricle	heart
23	chr11:18545600-18547400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr11:18545600-18547400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr11:18545600-18547400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:18546000-18547400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:18546200-18547400	Enhancers	Thymus	Thymus
28	chr11:18546400-18547400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr11:18546400-18547400	Weak transcription	Fetal Thymus	thymus
30	chr11:18546400-18547400	Enhancers	Hela-S3	cervix
31	chr11:18546600-18547400	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:18546600-18547800	Weak transcription	Small Intestine	intestine
33	chr11:18546800-18547400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:18546800-18547400	Weak transcription	Right Ventricle	heart
35	chr11:18547000-18547400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr11:18547000-18547400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr11:18547000-18547400	Enhancers	Primary T cells from cord blood	blood
38	chr11:18547000-18547400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr11:18547000-18547400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:18547000-18547400	Weak transcription	Fetal Intestine Small	intestine
41	chr11:18547000-18547600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:18547000-18547600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr11:18547000-18547600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr11:18547000-18547600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:18547000-18547800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:18547000-18547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:18547000-18547800	Weak transcription	Gastric	stomach
48	chr11:18547000-18547800	Weak transcription	Pancreas	Pancrea
49	chr11:18547000-18547800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:18547000-18547800	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links