Variant report

Variant	rs13385996
Chromosome Location	chr2:174077863-174077864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:174075523..174078423-chr2:174265356..174267374,2	K562	blood:
2	chr2:174065533..174067512-chr2:174076722..174079013,2	MCF-7	breast:
3	chr2:174076030..174078880-chr2:174080707..174082990,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10181133	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10182247	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10198981	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10497401	0.83[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11677913	0.90[YRI][hapmap]
rs11897681	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008554	0.91[CEU][hapmap]
rs13034748	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13035366	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13313780	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13430550	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13430650	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1371573	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1439977	0.91[YRI][hapmap]
rs16861404	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1866633	0.81[AFR][1000 genomes]
rs1866634	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289396	0.87[YRI][hapmap]
rs2289398	0.80[AFR][1000 genomes]
rs2358087	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28520717	0.81[ASN][1000 genomes]
rs3754740	0.97[ASN][1000 genomes]
rs3769165	0.89[CEU][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3769174	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3769177	0.89[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972535	0.84[CEU][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4972536	0.91[YRI][hapmap]
rs6734666	1.00[YRI][hapmap]
rs7566372	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13385996	ATF2	cis	cerebellum	SCAN
rs13385996	PDK1	cis	hippocampus	BrainEAC
rs13385996	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
2	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
3	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
4	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
5	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:174053400-174078400	Weak transcription	Gastric	stomach
7	chr2:174053400-174082000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:174053400-174089800	Weak transcription	Pancreas	Pancrea
9	chr2:174058000-174112800	Weak transcription	Spleen	Spleen
10	chr2:174060200-174092600	Weak transcription	Aorta	Aorta
11	chr2:174061000-174082000	Weak transcription	Fetal Brain Female	brain
12	chr2:174061200-174097600	Weak transcription	Lung	lung
13	chr2:174061400-174092200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:174061600-174083200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:174061600-174083200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:174061800-174080200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:174063600-174097600	Weak transcription	HSMM	muscle
18	chr2:174063800-174081600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:174063800-174083200	Weak transcription	GM12878-XiMat	blood
20	chr2:174063800-174095000	Weak transcription	Right Ventricle	heart
21	chr2:174064200-174082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:174064200-174083000	Weak transcription	HepG2	liver
23	chr2:174064200-174083400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:174064200-174097600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:174064600-174082000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:174064600-174083200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:174069400-174081800	Weak transcription	Ovary	ovary
28	chr2:174069400-174082200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:174069400-174097000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:174069400-174097600	Weak transcription	Primary B cells from cord blood	blood
31	chr2:174069600-174096600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:174070000-174081800	Weak transcription	Fetal Brain Male	brain
33	chr2:174071800-174094200	Weak transcription	Fetal Thymus	thymus
34	chr2:174072000-174078600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:174072200-174095400	Weak transcription	Right Atrium	heart
36	chr2:174073000-174078000	Weak transcription	Brain Germinal Matrix	brain
37	chr2:174075000-174078200	Weak transcription	HMEC	breast
38	chr2:174075200-174078400	Strong transcription	Left Ventricle	heart
39	chr2:174075400-174078400	Weak transcription	Liver	Liver
40	chr2:174075400-174082000	Weak transcription	NHLF	lung
41	chr2:174075400-174097600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:174075600-174078800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:174075600-174080800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:174075600-174083000	Weak transcription	Fetal Kidney	kidney
45	chr2:174075800-174081600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:174075800-174081600	Weak transcription	Fetal Lung	lung
47	chr2:174075800-174081800	Weak transcription	NH-A	brain
48	chr2:174075800-174082800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:174075800-174082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:174075800-174083000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links