Variant report

Variant	rs11885883
Chromosome Location	chr2:99354491-99354492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99352512..99355304-chr2:99377484..99380437,2	MCF-7	breast:
2	chr2:99097067..99098913-chr2:99352317..99355051,2	MCF-7	breast:
3	chr2:99352944..99355702-chr2:99450894..99453779,2	MCF-7	breast:
4	chr2:99344987..99348857-chr2:99353398..99358314,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1016124	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10173832	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10177696	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10194177	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10200288	0.95[ASN][1000 genomes]
rs10210711	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10496332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123749	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123751	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12471383	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12477450	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12615301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993424	0.96[ASN][1000 genomes]
rs13391483	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514916	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1517681	0.96[ASN][1000 genomes]
rs1913621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013983	0.96[ASN][1000 genomes]
rs28783173	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34521960	0.96[ASN][1000 genomes]
rs35477458	0.96[ASN][1000 genomes]
rs41445250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851153	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851154	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58666702	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6712597	0.80[ASN][1000 genomes]
rs6740656	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7420869	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581128	0.82[CHB][hapmap]
rs7599792	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs885036	0.81[CHB][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
2	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
3	chr2:99348800-99360600	Weak transcription	Lung	lung
4	chr2:99349200-99357200	Enhancers	HepG2	liver
5	chr2:99349400-99355800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:99349800-99355200	Enhancers	Fetal Thymus	thymus
7	chr2:99351200-99355600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:99351400-99355000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:99351400-99355800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr2:99351600-99355000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:99351600-99355800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:99351800-99354600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr2:99351800-99355200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:99351800-99355200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:99351800-99355400	Enhancers	Primary T cells from cord blood	blood
16	chr2:99351800-99355800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:99351800-99356200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:99351800-99356600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:99351800-99356600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:99351800-99360400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:99351800-99360600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:99352600-99355200	Enhancers	Small Intestine	intestine
23	chr2:99352800-99359000	Weak transcription	Placenta	Placenta
24	chr2:99352800-99360400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:99353200-99356800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:99353400-99354800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:99353400-99358000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:99353400-99359400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:99353400-99360400	Weak transcription	HMEC	breast
30	chr2:99353600-99355200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:99353600-99355600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:99353600-99359400	Weak transcription	HUVEC	blood vessel
33	chr2:99353800-99355200	Enhancers	Gastric	stomach
34	chr2:99353800-99355600	Enhancers	Pancreas	Pancrea
35	chr2:99354000-99359400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:99354400-99354600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:99354400-99354600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:99354400-99354600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:99354400-99354600	Enhancers	Stomach Mucosa	stomach
40	chr2:99354400-99354800	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:99354400-99354800	Enhancers	Dnd41	blood
42	chr2:99354400-99355000	Enhancers	Thymus	Thymus

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