Variant report

Variant	rs6432129
Chromosome Location	chr2:10790410-10790411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10787792..10790462-chr2:10909882..10911880,2	K562	blood:
2	chr2:10788856..10790515-chr2:10797062..10799829,2	K562	blood:
3	chr2:10787086..10789561-chr2:10790205..10792543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272275	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10207845	0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1023587	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1023588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1045596	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs10490187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929675	1.00[CEU][hapmap]
rs11673879	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11681219	0.91[EUR][1000 genomes]
rs12476022	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621903	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12998328	1.00[CEU][hapmap]
rs13011439	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs13019722	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13035291	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1990614	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2015525	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2110779	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2160257	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs2287063	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34140737	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34562923	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34565728	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34851538	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34965800	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35364825	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35454548	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35688901	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36065209	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3732111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732114	1.00[CEU][hapmap]
rs3815520	0.96[CHB][hapmap]
rs3821195	0.96[CHB][hapmap]
rs3821196	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4668688	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs4668692	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4669597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669600	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4669601	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56403646	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56902481	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59199925	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62127163	0.91[EUR][1000 genomes]
rs62127196	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6432106	0.89[EUR][1000 genomes]
rs6432108	0.91[EUR][1000 genomes]
rs6432127	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6716907	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6733161	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6744848	0.95[CHB][hapmap]
rs6748865	1.00[CEU][hapmap]
rs6752034	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6752145	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6757809	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs7579314	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7594513	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7594805	0.95[CHB][hapmap]
rs7594816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9678985	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10725600-10793400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:10729400-10798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:10742600-10791000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:10753600-10792800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:10754800-10796000	Weak transcription	Small Intestine	intestine
6	chr2:10756200-10795800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:10756200-10828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:10761800-10793600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:10762000-10793600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:10771800-10793400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:10772200-10793400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:10772200-10808400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:10772400-10793600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:10775000-10793000	Weak transcription	Psoas Muscle	Psoas
15	chr2:10775000-10793800	Weak transcription	Stomach Mucosa	stomach
16	chr2:10775000-10794200	Weak transcription	HUVEC	blood vessel
17	chr2:10776200-10793600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:10776200-10803000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:10778400-10793000	Weak transcription	Brain Substantia Nigra	brain
20	chr2:10779400-10801400	Strong transcription	Primary T cells from cord blood	blood
21	chr2:10779600-10803600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:10779600-10808400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:10780600-10790600	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:10780600-10800000	Weak transcription	Right Atrium	heart
25	chr2:10781600-10792200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:10781600-10799800	Strong transcription	Liver	Liver
27	chr2:10781600-10800400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:10781800-10803000	Strong transcription	Adipose Nuclei	Adipose
29	chr2:10782000-10803200	Strong transcription	Dnd41	blood
30	chr2:10782200-10808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:10782600-10794400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:10783200-10790800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:10783600-10791000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:10783800-10791000	Weak transcription	NHDF-Ad	bronchial
35	chr2:10784200-10790800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:10784200-10792800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:10784200-10793400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:10784200-10793600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:10784200-10793600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:10784400-10790800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:10784600-10790600	Weak transcription	Thymus	Thymus
42	chr2:10784800-10803200	Strong transcription	A549	lung
43	chr2:10785800-10791600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:10785800-10800200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:10786000-10800400	Strong transcription	HepG2	liver
46	chr2:10786000-10800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:10786200-10792000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:10786200-10800400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:10786200-10802800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:10786200-10803600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links