Variant report

Variant	rs12469875
Chromosome Location	chr2:173304036-173304037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173294248..173297165-chr2:173302746..173304421,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10171775	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10175670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10184567	0.87[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10195932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10197251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10497381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10497385	1.00[CEU][hapmap]
rs1076595	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12465295	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12465442	1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs12467358	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs12477247	1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs12477594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12622044	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16860377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16860497	0.80[MEX][hapmap]
rs16860543	1.00[CEU][hapmap]
rs2293646	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2357415	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs28464102	0.82[ASN][1000 genomes]
rs28540552	0.87[ASN][1000 genomes]
rs3749148	0.81[JPT][hapmap]
rs3762619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs3934627	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4281870	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4480959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4993282	0.85[ASN][1000 genomes]
rs4993283	0.85[ASN][1000 genomes]
rs6718477	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs6721597	0.84[ASN][1000 genomes]
rs6755100	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs7567159	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7604441	0.87[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3458704	chr2:173302313-173304582	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3458702	chr2:173302340-173304579	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv3458703	chr2:173302380-173304529	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv3458705	chr2:173302491-173304471	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173306400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
3	chr2:173295200-173306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:173295200-173306600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
6	chr2:173296000-173305600	Weak transcription	Fetal Lung	lung
7	chr2:173296000-173307600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr2:173296200-173305000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:173296200-173307600	Enhancers	Fetal Thymus	thymus
10	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:173297000-173306600	Enhancers	Small Intestine	intestine
12	chr2:173297000-173307600	Enhancers	Pancreas	Pancrea
13	chr2:173297200-173304800	Weak transcription	Fetal Kidney	kidney
14	chr2:173297600-173307400	Enhancers	Spleen	Spleen
15	chr2:173299200-173305000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr2:173299800-173304200	Enhancers	Psoas Muscle	Psoas
17	chr2:173300200-173304600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:173300200-173307600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:173300400-173305000	Enhancers	Lung	lung
20	chr2:173300400-173308000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:173300600-173306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:173300800-173304800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
24	chr2:173301200-173305600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:173301200-173305800	Weak transcription	Fetal Heart	heart
26	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:173301400-173304800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:173301600-173305000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr2:173301600-173305400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr2:173301800-173305600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:173301800-173305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:173302000-173304800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:173302000-173305000	Transcr. at gene 5' and 3'	NHEK	skin
35	chr2:173302400-173304800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:173302400-173304800	Enhancers	Esophagus	oesophagus
37	chr2:173302400-173307600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:173302400-173308200	Enhancers	HepG2	liver
39	chr2:173302600-173304200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:173302600-173304200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:173302600-173304600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:173302600-173308000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr2:173302800-173304200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:173302800-173304600	Enhancers	Brain Substantia Nigra	brain
45	chr2:173302800-173304800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:173303000-173304200	Enhancers	Brain Hippocampus Middle	brain
47	chr2:173303000-173304600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:173303000-173304600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:173303000-173305000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:173303000-173305000	Enhancers	Colonic Mucosa	Colon

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