Variant report

Variant	rs12037599
Chromosome Location	chr1:9786845-9786846
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9785533..9787821-chr1:9792843..9795633,2	MCF-7	breast:
2	chr1:9784387..9786880-chr1:9870981..9873040,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10779730	0.80[EUR][1000 genomes]
rs10779731	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs10864436	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11121485	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11121488	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121492	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11121493	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1141402	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804356	0.80[EUR][1000 genomes]
rs12025864	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12034239	0.85[ASN][1000 genomes]
rs12034313	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047054	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs12078414	0.85[CEU][hapmap]
rs12564733	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12568720	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs12569008	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs1615629	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1660741	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1660742	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs17034335	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17034340	0.85[ASN][1000 genomes]
rs1767277	0.85[CEU][hapmap]
rs41280774	0.91[EUR][1000 genomes]
rs41280776	0.91[EUR][1000 genomes]
rs4512653	0.88[CHB][hapmap]
rs6699320	0.85[CEU][hapmap]
rs7526958	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7550295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767762	0.85[CEU][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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
3	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:9777800-9790200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:9777800-9790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:9778400-9793400	Weak transcription	Fetal Kidney	kidney
7	chr1:9778600-9788400	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr1:9778600-9790600	Weak transcription	Small Intestine	intestine
9	chr1:9779000-9788600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:9780000-9790800	Weak transcription	Hela-S3	cervix
11	chr1:9780600-9792600	Strong transcription	Dnd41	blood
12	chr1:9781200-9790200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:9781200-9813200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:9781600-9800600	Weak transcription	Fetal Brain Male	brain
15	chr1:9781800-9788200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:9781800-9793600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:9782000-9788400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:9782200-9792800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:9782800-9788400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:9783000-9787200	Weak transcription	HSMMtube	muscle
21	chr1:9783800-9787000	Weak transcription	Colonic Mucosa	Colon
22	chr1:9783800-9787000	Weak transcription	Right Ventricle	heart
23	chr1:9783800-9787600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:9783800-9788600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:9783800-9789800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:9783800-9799600	Strong transcription	Fetal Brain Female	brain
27	chr1:9784000-9787000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:9784000-9787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:9784000-9787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:9784000-9787600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:9784000-9789000	Weak transcription	Brain Angular Gyrus	brain
32	chr1:9784000-9789000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:9784000-9789000	Weak transcription	NHDF-Ad	bronchial
34	chr1:9784000-9790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:9784000-9793400	Strong transcription	Brain Germinal Matrix	brain
36	chr1:9784000-9797200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:9784000-9815400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:9784200-9787000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:9784200-9787200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:9784200-9787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:9784200-9787400	Weak transcription	HSMM	muscle
42	chr1:9784200-9787600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:9784200-9788200	Weak transcription	Pancreas	Pancrea
44	chr1:9784200-9788600	Weak transcription	Aorta	Aorta
45	chr1:9784200-9788600	Weak transcription	Brain Substantia Nigra	brain
46	chr1:9784200-9789000	Weak transcription	NHLF	lung
47	chr1:9784200-9789200	Weak transcription	Fetal Lung	lung
48	chr1:9784200-9789400	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:9784200-9792600	Strong transcription	Fetal Stomach	stomach
50	chr1:9784200-9796800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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