Variant report

Variant	rs13395498
Chromosome Location	chr2:47204496-47204497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47167461..47169104-chr2:47203278..47205346,2	MCF-7	breast:
2	chr2:47201349..47204560-chr2:47402246..47404711,3	K562	blood:
3	chr2:47202754..47204715-chr2:47226558..47228586,2	K562	blood:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10183233	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs11125106	0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs11125107	0.85[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs11125108	0.84[ASN][1000 genomes]
rs11680029	0.85[ASN][1000 genomes]
rs11681157	0.81[ASN][1000 genomes]
rs11685605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11883507	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs12712984	0.81[CHB][hapmap]
rs13002842	0.83[ASN][1000 genomes]
rs13406452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1433772	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1433773	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17480779	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1865262	0.81[ASN][1000 genomes]
rs2241736	0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs2347260	0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2881587	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs35779609	0.84[ASN][1000 genomes]
rs4952856	0.83[AMR][1000 genomes]
rs4952858	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4953437	0.81[JPT][hapmap]
rs6716882	0.92[ASN][1000 genomes]
rs6731862	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6731875	0.87[ASN][1000 genomes]
rs6734201	0.83[ASN][1000 genomes]
rs736683	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs746915	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs7558171	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7558196	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7560371	0.94[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs877047	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs877048	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs892381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs993847	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:47186800-47205200	Weak transcription	Gastric	stomach
12	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain
14	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:47188000-47205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:47188000-47207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:47195600-47205200	Weak transcription	Fetal Lung	lung
18	chr2:47195600-47210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:47195600-47212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:47196000-47205800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:47196400-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:47196600-47227800	Strong transcription	Dnd41	blood
23	chr2:47197600-47206000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:47198000-47209800	Weak transcription	Right Atrium	heart
25	chr2:47198200-47205800	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:47198200-47206800	Weak transcription	Right Ventricle	heart
27	chr2:47198400-47208000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:47199200-47208600	Weak transcription	Small Intestine	intestine
29	chr2:47199400-47208400	Weak transcription	HUVEC	blood vessel
30	chr2:47199600-47209600	Strong transcription	Osteobl	bone
31	chr2:47199800-47208400	Strong transcription	Fetal Intestine Small	intestine
32	chr2:47199800-47209600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:47200000-47205200	Weak transcription	Pancreas	Pancrea
34	chr2:47200000-47207800	Strong transcription	HepG2	liver
35	chr2:47200000-47207800	Weak transcription	K562	blood
36	chr2:47200200-47204600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:47200200-47205000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:47200200-47208000	Weak transcription	Stomach Mucosa	stomach
39	chr2:47200200-47210000	Weak transcription	Hela-S3	cervix
40	chr2:47200400-47208800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:47200600-47205200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:47200800-47216400	Genic enhancers	Fetal Thymus	thymus
43	chr2:47201400-47204600	Strong transcription	Thymus	Thymus
44	chr2:47201400-47209400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:47201600-47205200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:47201600-47206200	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:47201600-47208600	Strong transcription	A549	lung
48	chr2:47201600-47210200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:47201600-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:47201600-47213200	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links