Variant report

Variant	rs2140709
Chromosome Location	chr1:151036816-151036817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150996357..150999455-chr1:151032530..151036839,3	K562	blood:

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10749659	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10788798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788799	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039334	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12039542	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12040729	0.80[AFR][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12117163	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12134957	0.81[ASN][1000 genomes]
rs12569193	0.86[JPT][hapmap]
rs1524773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15740	0.84[CEU][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs1969442	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2067606	1.00[JPT][hapmap]
rs2902810	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3738481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806386	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806387	0.89[CEU][hapmap];0.88[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4357530	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4512652	0.86[JPT][hapmap]
rs4970939	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970941	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4970993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970998	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970999	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971002	0.84[ASN][1000 genomes]
rs4971003	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971006	0.84[ASN][1000 genomes]
rs4971007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971008	0.89[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs6587552	0.81[CHD][hapmap]
rs6587553	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6587557	0.86[JPT][hapmap]
rs6656450	0.86[JPT][hapmap]
rs6657593	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6668894	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674970	0.86[JPT][hapmap]
rs6676190	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6694158	1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7366148	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7523731	1.00[JPT][hapmap]
rs7532312	1.00[CHB][hapmap]
rs7540258	1.00[CHB][hapmap]
rs7550434	1.00[CHB][hapmap]
rs7554936	1.00[JPT][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2140709	ZNF687	cis	cerebellum	SCAN
rs2140709	CDC42SE1	cis	lymphoblastoid	seeQTL
rs2140709	MRPS21	cis	cerebellum	SCAN
rs2140709	CDC42SE1	cis	multi-tissue	Pritchard
rs2140709	PGLYRP4	cis	parietal	SCAN
rs2140709	BNIPL	cis	Thyroid	GTEx
rs2140709	BNIPL	cis	multi-tissue	Pritchard
rs2140709	RPTN	cis	cerebellum	SCAN
rs2140709	GABPB2	cis	cerebellum	SCAN
rs2140709	BNIPL	cis	lung	GTEx
rs2140709	PRPF3	cis	parietal	SCAN
rs2140709	CDC42SE1	cis	parietal	SCAN
rs2140709	MRPS21	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151033000-151042800	Weak transcription	Gastric	stomach
2	chr1:151033200-151042200	Weak transcription	Esophagus	oesophagus
3	chr1:151033200-151042200	Weak transcription	Pancreas	Pancrea
4	chr1:151033200-151042600	Weak transcription	Aorta	Aorta
5	chr1:151033600-151041800	Weak transcription	Primary B cells from cord blood	blood
6	chr1:151033600-151042200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:151033800-151038400	Weak transcription	Primary T cells from cord blood	blood
8	chr1:151033800-151042600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:151033800-151042600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:151033800-151042600	Weak transcription	Right Atrium	heart
11	chr1:151034000-151038200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:151034000-151038400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:151034000-151041800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:151034000-151041800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:151034000-151041800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:151034000-151042000	Weak transcription	Spleen	Spleen
17	chr1:151034000-151042200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:151034000-151042400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:151034200-151038400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:151034200-151038400	Weak transcription	Fetal Stomach	stomach
21	chr1:151034200-151038600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:151034200-151041600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:151034200-151042400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:151034400-151038600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:151034400-151041400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:151034400-151042200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:151034600-151037000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:151034600-151038600	Weak transcription	Thymus	Thymus
29	chr1:151034600-151039600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:151034600-151041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:151034600-151042600	Weak transcription	Fetal Kidney	kidney
32	chr1:151034800-151037000	Weak transcription	Liver	Liver
33	chr1:151035200-151037200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
34	chr1:151035200-151037600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151035200-151041600	Strong transcription	Fetal Thymus	thymus
36	chr1:151035400-151037200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
37	chr1:151035400-151037400	Genic enhancers	K562	blood
38	chr1:151035400-151038400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:151035400-151038400	Weak transcription	Fetal Lung	lung
40	chr1:151035400-151038800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:151035800-151037000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:151035800-151037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:151035800-151037000	Genic enhancers	HUVEC	blood vessel
44	chr1:151035800-151037400	Strong transcription	HSMM	muscle
45	chr1:151035800-151039600	Weak transcription	NHLF	lung
46	chr1:151035800-151039800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:151035800-151041800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:151035800-151041800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:151035800-151041800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:151035800-151042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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