Variant report

Variant	rs12713810
Chromosome Location	chr2:74320262-74320263
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74311799..74313643-chr2:74317613..74320448,2	K562	blood:
2	chr2:74209051..74213091-chr2:74319558..74323608,5	MCF-7	breast:
3	chr2:74187721..74190060-chr2:74320133..74322704,2	K562	blood:
4	chr2:74209608..74214006-chr2:74318475..74321886,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255989	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10164943	0.95[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168249	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10168408	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10168410	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10179742	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10179967	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10186781	0.89[ASN][1000 genomes]
rs10191539	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10192993	0.89[ASN][1000 genomes]
rs10198884	1.00[JPT][hapmap]
rs10200470	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11126424	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11884748	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11885172	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11886928	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11898903	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12328927	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713804	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs12713805	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713806	0.90[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713808	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713809	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12988533	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12995468	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs13005103	0.88[EUR][1000 genomes]
rs13006301	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13006407	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13011961	0.88[EUR][1000 genomes]
rs13013211	0.91[EUR][1000 genomes]
rs13014576	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13016198	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs13021880	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13027288	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13027623	0.82[EUR][1000 genomes]
rs13030414	0.82[EUR][1000 genomes]
rs13387010	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13387412	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13396777	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13413697	0.89[ASN][1000 genomes]
rs13426799	0.89[ASN][1000 genomes]
rs28450901	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34136450	0.90[EUR][1000 genomes]
rs34201525	0.89[EUR][1000 genomes]
rs35592918	0.83[EUR][1000 genomes]
rs35609589	0.83[EUR][1000 genomes]
rs3902790	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241260	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4328662	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4331526	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4338985	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4364046	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4371381	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4374402	0.83[EUR][1000 genomes]
rs4416242	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4574138	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4578887	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4621184	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4852326	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853003	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853005	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853006	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853007	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853009	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60279245	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546884	0.82[EUR][1000 genomes]
rs6546885	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6546886	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6546887	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546889	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6706327	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6714186	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6717896	0.86[CEU][hapmap]
rs6741544	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743073	0.82[EUR][1000 genomes]
rs6745236	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745576	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6745792	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754218	0.87[EUR][1000 genomes]
rs6755711	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6756474	0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71337722	0.87[EUR][1000 genomes]
rs7560668	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568898	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7584777	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585240	0.86[CEU][hapmap]
rs7587991	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7589915	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7592749	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7593050	0.95[CEU][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs7595401	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7597388	0.88[EUR][1000 genomes]
rs7601526	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606491	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309478	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12713810	SLC4A5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74269800-74328000	Weak transcription	Psoas Muscle	Psoas
2	chr2:74298400-74320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:74299800-74332000	Strong transcription	Dnd41	blood
4	chr2:74299800-74333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:74300000-74333200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:74300800-74333600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:74303200-74321000	Weak transcription	Fetal Brain Male	brain
8	chr2:74306000-74332400	Strong transcription	Fetal Intestine Small	intestine
9	chr2:74306400-74332000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:74306800-74323000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:74306800-74323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:74306800-74323600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:74306800-74323600	Strong transcription	Brain Germinal Matrix	brain
14	chr2:74306800-74323600	Strong transcription	Fetal Intestine Large	intestine
15	chr2:74306800-74330400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:74307000-74324200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:74307000-74332600	Strong transcription	Primary T cells from cord blood	blood
18	chr2:74307200-74331800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:74307200-74332600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:74307200-74333000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:74307400-74322600	Strong transcription	Fetal Brain Female	brain
22	chr2:74307400-74323600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:74307400-74325200	Strong transcription	Fetal Thymus	thymus
24	chr2:74307400-74326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:74307400-74330400	Strong transcription	Thymus	Thymus
26	chr2:74307600-74322800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:74307600-74323600	Strong transcription	Liver	Liver
28	chr2:74307600-74326000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:74307600-74331000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:74307600-74332000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr2:74307600-74333400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:74308000-74323000	Strong transcription	Adipose Nuclei	Adipose
33	chr2:74308200-74332600	Strong transcription	GM12878-XiMat	blood
34	chr2:74308400-74336200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:74308600-74323000	Strong transcription	Spleen	Spleen
36	chr2:74308600-74325000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr2:74308600-74333200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:74309200-74321600	Weak transcription	NHDF-Ad	bronchial
39	chr2:74309600-74323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:74311200-74321600	Weak transcription	Hela-S3	cervix
41	chr2:74311200-74326400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:74312200-74322400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:74312200-74322600	Strong transcription	NHEK	skin
44	chr2:74312200-74325000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:74312200-74333800	Strong transcription	Fetal Stomach	stomach
46	chr2:74313600-74322600	Strong transcription	Right Ventricle	heart
47	chr2:74313600-74323000	Strong transcription	Fetal Lung	lung
48	chr2:74314000-74322600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:74314000-74323200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr2:74314200-74320800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links