Variant report

Variant	rs3105099
Chromosome Location	chr2:95707519-95707520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95698656..95702870-chr2:95706305..95711036,7	MCF-7	breast:
2	chr2:95706431..95707932-chr2:95711517..95713440,2	MCF-7	breast:
3	chr2:95686313..95689732-chr2:95706916..95710668,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17119148	0.82[JPT][hapmap]
rs1875402	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs2291991	0.90[ASN][1000 genomes]
rs2320620	0.86[YRI][hapmap]
rs3105098	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3105101	0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3105104	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3105105	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs3112225	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs3112228	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3112230	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs3112982	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112983	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3112984	0.84[ASN][1000 genomes]
rs3112985	0.89[ASW][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.82[ASN][1000 genomes]
rs3112986	0.88[ASW][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs3112995	0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3112996	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3112997	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs3113002	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4241315	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs4854241	0.85[GIH][hapmap]
rs62637956	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6725821	0.89[ASW][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs7560571	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap]
rs7565772	0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap]
rs7582368	0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs872580	0.89[ASW][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[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	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS 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
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv3326687	chr2:95700225-95708023	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv3444058	chr2:95700825-95707523	Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95698400-95710400	Enhancers	Brain Substantia Nigra	brain
2	chr2:95699000-95708200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:95699200-95710000	Enhancers	Brain Anterior Caudate	brain
4	chr2:95700000-95710200	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:95700200-95708000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:95700200-95709000	Enhancers	Brain Hippocampus Middle	brain
7	chr2:95700400-95709000	Weak transcription	Dnd41	blood
8	chr2:95701200-95708200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:95702600-95707800	Weak transcription	Pancreas	Pancrea
10	chr2:95702600-95711200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:95703000-95712400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:95704600-95707600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:95704600-95707800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:95704600-95708200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:95705400-95708800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:95705600-95707800	Enhancers	HSMMtube	muscle
17	chr2:95705600-95708000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:95705600-95708800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:95705800-95719000	Enhancers	GM12878-XiMat	blood
20	chr2:95705800-95721600	Genic enhancers	Fetal Thymus	thymus
21	chr2:95706000-95707800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:95706200-95707600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:95706200-95707800	Weak transcription	Esophagus	oesophagus
24	chr2:95706200-95708200	Weak transcription	Gastric	stomach
25	chr2:95706200-95708800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:95706200-95709000	Enhancers	Placenta	Placenta
27	chr2:95706200-95723800	Weak transcription	Fetal Kidney	kidney
28	chr2:95706400-95708000	Weak transcription	Lung	lung
29	chr2:95706400-95708200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:95706400-95708600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:95706400-95708600	Weak transcription	Fetal Heart	heart
32	chr2:95706400-95708800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:95706400-95709600	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:95706400-95710600	Enhancers	Fetal Muscle Leg	muscle
35	chr2:95706400-95717600	Genic enhancers	Thymus	Thymus
36	chr2:95706600-95708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:95706600-95708600	Weak transcription	Spleen	Spleen
38	chr2:95706600-95709400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:95706600-95710600	Enhancers	Stomach Mucosa	stomach
40	chr2:95706800-95709200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:95706800-95709400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:95707000-95707800	Weak transcription	Left Ventricle	heart
43	chr2:95707000-95707800	Weak transcription	Right Atrium	heart
44	chr2:95707000-95708200	Weak transcription	Right Ventricle	heart
45	chr2:95707200-95707600	Weak transcription	Fetal Lung	lung
46	chr2:95707200-95709800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:95707200-95710200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:95707400-95708600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:95707400-95708600	Enhancers	HSMM	muscle
50	chr2:95707400-95708800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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