Variant report

Variant	rs2163336
Chromosome Location	chr2:10110517-10110518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10102444..10109047-chr2:10109192..10115495,9	MCF-7	breast:
2	chr2:10105826..10108731-chr2:10110445..10113153,2	K562	blood:
3	chr2:10100605..10103571-chr2:10109016..10111061,2	MCF-7	breast:
4	chr2:10109306..10112948-chr2:10113189..10116781,5	MCF-7	breast:
5	chr2:10110373..10112449-chr2:10116359..10118235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11674576	0.94[ASN][1000 genomes]
rs11690988	0.94[ASN][1000 genomes]
rs11883961	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs11886114	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11886486	0.94[ASN][1000 genomes]
rs11887890	0.94[ASN][1000 genomes]
rs11889061	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs11902236	0.83[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11902932	0.94[ASN][1000 genomes]
rs13401891	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16867262	0.82[CHB][hapmap];0.92[ASN][1000 genomes]
rs16867266	0.82[CHB][hapmap];0.92[ASN][1000 genomes]
rs16867274	0.82[ASW][hapmap];0.81[YRI][hapmap]
rs17455130	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs1897164	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs2003911	0.94[ASN][1000 genomes]
rs2012320	0.92[ASN][1000 genomes]
rs2116014	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791761	0.85[ASN][1000 genomes]
rs3791763	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs3791764	0.94[ASN][1000 genomes]
rs3828262	0.86[ASN][1000 genomes]
rs41264205	0.94[ASN][1000 genomes]
rs4482455	0.89[ASN][1000 genomes]
rs4635506	0.89[ASN][1000 genomes]
rs59345896	0.94[ASN][1000 genomes]
rs66920316	0.94[ASN][1000 genomes]
rs67093290	0.94[ASN][1000 genomes]
rs6711126	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs6716765	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs6721359	0.94[ASN][1000 genomes]
rs67223835	0.94[ASN][1000 genomes]
rs6725087	0.94[ASN][1000 genomes]
rs6735737	0.89[ASN][1000 genomes]
rs6739827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749296	0.94[ASN][1000 genomes]
rs6750565	0.94[ASN][1000 genomes]
rs6750946	0.94[ASN][1000 genomes]
rs72784430	0.87[ASN][1000 genomes]
rs72784434	0.94[ASN][1000 genomes]
rs72784441	0.94[ASN][1000 genomes]
rs72784463	0.94[ASN][1000 genomes]
rs730922	0.94[ASN][1000 genomes]
rs73162262	0.94[ASN][1000 genomes]
rs73162264	0.94[ASN][1000 genomes]
rs73913937	0.94[ASN][1000 genomes]
rs73913938	0.94[ASN][1000 genomes]
rs891499	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10092600-10112600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:10092600-10113400	Weak transcription	Left Ventricle	heart
3	chr2:10092800-10110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:10093200-10110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:10093600-10112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
7	chr2:10095000-10112600	Weak transcription	Hela-S3	cervix
8	chr2:10099000-10115400	Strong transcription	Liver	Liver
9	chr2:10101000-10113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:10101000-10117000	Strong transcription	HepG2	liver
11	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:10101600-10110600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:10101600-10113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:10101600-10116400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
16	chr2:10101800-10114800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:10102200-10110600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:10102400-10116600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:10104600-10130200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:10104800-10110600	Weak transcription	Psoas Muscle	Psoas
22	chr2:10104800-10112600	Weak transcription	Fetal Intestine Small	intestine
23	chr2:10104800-10112600	Weak transcription	Gastric	stomach
24	chr2:10105600-10111000	Weak transcription	Fetal Kidney	kidney
25	chr2:10106000-10112600	Weak transcription	Pancreas	Pancrea
26	chr2:10106000-10119800	Weak transcription	Dnd41	blood
27	chr2:10107400-10111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:10107800-10112400	Weak transcription	Stomach Mucosa	stomach
29	chr2:10109000-10112000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:10109400-10110800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:10109400-10112400	Weak transcription	Esophagus	oesophagus
32	chr2:10109400-10112600	Weak transcription	K562	blood
33	chr2:10109400-10115600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:10109600-10112600	Weak transcription	Lung	lung
35	chr2:10109600-10112800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:10109600-10112800	Weak transcription	Fetal Thymus	thymus
37	chr2:10110200-10111000	Enhancers	Colon Smooth Muscle	Colon
38	chr2:10110200-10117800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:10110400-10110600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:10110400-10110600	Enhancers	Aorta	Aorta
41	chr2:10110400-10110800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:10110400-10110800	Genic enhancers	Placenta	Placenta
43	chr2:10110400-10111000	Enhancers	Adipose Nuclei	Adipose
44	chr2:10110400-10111000	Enhancers	Fetal Heart	heart
45	chr2:10110400-10111000	Enhancers	Fetal Muscle Leg	muscle
46	chr2:10110400-10111000	Enhancers	Fetal Stomach	stomach
47	chr2:10110400-10112000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:10110400-10113200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:10110400-10113400	Enhancers	Ovary	ovary
50	chr2:10110400-10113600	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links