Variant report

Variant	rs12202501
Chromosome Location	chr6:44085028-44085029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44084290..44087287-chr6:44233720..44236514,2	K562	blood:
2	chr6:44076515..44082841-chr6:44082960..44087705,9	MCF-7	breast:
3	chr6:44084698..44087576-chr6:44213851..44216783,3	K562	blood:
4	chr6:44042412..44044221-chr6:44084102..44086584,2	K562	blood:
5	chr6:44084752..44087576-chr6:44214784..44216783,2	K562	blood:
6	chr6:44081901..44085348-chr6:44213567..44215363,3	MCF-7	breast:
7	chr6:44083043..44086342-chr6:44189537..44193690,3	K562	blood:

Variant related genes	Relation type
ENSG00000096384	Chromatin interaction
ENSG00000112759	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10948121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12191873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12199128	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206251	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206795	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236061	1.00[AFR][1000 genomes]
rs3734695	0.94[JPT][hapmap]
rs3734696	0.97[EUR][1000 genomes]
rs3734697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4628095	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711766	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714738	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4714750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714761	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4714762	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62401766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62403189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs877112	1.00[JPT][hapmap]
rs9349270	1.00[AFR][1000 genomes]
rs9349271	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349272	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369448	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369456	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369457	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369458	0.94[JPT][hapmap]
rs9369459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381287	1.00[AFR][1000 genomes]
rs9381294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44058800-44093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44066000-44091000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:44071200-44086400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:44074000-44086600	Strong transcription	Fetal Stomach	stomach
5	chr6:44077800-44086200	Genic enhancers	HepG2	liver
6	chr6:44081800-44085400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:44081800-44087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:44081800-44093600	Weak transcription	Brain Substantia Nigra	brain
9	chr6:44082000-44088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:44082000-44090800	Weak transcription	Spleen	Spleen
11	chr6:44082200-44087400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:44082200-44087800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:44082200-44087800	Weak transcription	Primary B cells from cord blood	blood
14	chr6:44082200-44093600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:44082400-44087800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:44082400-44088000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:44082400-44090400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:44082800-44089400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:44083000-44085200	Enhancers	Gastric	stomach
20	chr6:44083000-44085400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:44083000-44086200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:44083000-44086400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:44083000-44086800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:44083000-44087000	Enhancers	HUVEC	blood vessel
25	chr6:44083200-44086400	Genic enhancers	K562	blood
26	chr6:44083200-44093800	Weak transcription	Fetal Brain Male	brain
27	chr6:44083400-44085400	Genic enhancers	Fetal Muscle Leg	muscle
28	chr6:44083400-44085600	Genic enhancers	Thymus	Thymus
29	chr6:44083400-44086400	Genic enhancers	Fetal Intestine Small	intestine
30	chr6:44083400-44086400	Genic enhancers	Fetal Thymus	thymus
31	chr6:44083400-44086600	Enhancers	Liver	Liver
32	chr6:44083400-44087600	Weak transcription	Brain Angular Gyrus	brain
33	chr6:44083400-44090400	Weak transcription	Fetal Kidney	kidney
34	chr6:44083600-44085200	Enhancers	Adipose Nuclei	Adipose
35	chr6:44083600-44085200	Enhancers	Fetal Lung	lung
36	chr6:44083600-44085400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:44083600-44090400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:44083600-44090800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:44083600-44092600	Enhancers	HMEC	breast
40	chr6:44083800-44085200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:44083800-44085400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr6:44083800-44085600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:44083800-44087800	Weak transcription	Lung	lung
44	chr6:44083800-44088400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:44083800-44090400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:44083800-44093800	Enhancers	Stomach Mucosa	stomach
47	chr6:44084000-44085200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:44084000-44085200	Enhancers	Aorta	Aorta
49	chr6:44084000-44085400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr6:44084000-44085600	Enhancers	Colonic Mucosa	Colon

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