Variant report

Variant	rs7599043
Chromosome Location	chr2:98505730-98505731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98505348..98508247-chr2:98519250..98521290,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10166513	1.00[ASN][1000 genomes]
rs10167772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168543	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168709	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10169155	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10175129	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176826	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10180434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180837	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10183768	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184393	0.88[EUR][1000 genomes]
rs10184457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10184552	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10188497	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191101	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10191483	1.00[JPT][hapmap]
rs10192322	0.89[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10202138	1.00[ASN][1000 genomes]
rs10206684	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208070	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10209970	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10210299	0.84[EUR][1000 genomes]
rs10210520	0.94[ASN][1000 genomes]
rs10210880	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1024086	0.85[CHB][hapmap]
rs11886417	0.94[ASN][1000 genomes]
rs11893437	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11894541	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894895	0.94[ASN][1000 genomes]
rs11895170	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11897301	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712117	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712120	0.94[ASN][1000 genomes]
rs12712147	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712162	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712163	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12712172	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992955	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004862	0.83[ASN][1000 genomes]
rs13008678	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13008904	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010004	0.94[ASN][1000 genomes]
rs13012645	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13387725	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13404788	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13427422	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1446327	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503202	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1960329	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982336	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2121271	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293679	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2305142	0.85[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs34190123	1.00[ASN][1000 genomes]
rs34305873	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34414288	0.94[ASN][1000 genomes]
rs34469351	0.90[ASN][1000 genomes]
rs35185431	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35203092	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35402416	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35776557	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35807655	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940587	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36079497	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821053	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55753459	1.00[ASN][1000 genomes]
rs55817781	0.83[EUR][1000 genomes]
rs6543088	0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs6543111	0.91[ASN][1000 genomes]
rs6707719	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6707750	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6712078	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6713504	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6718982	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721323	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721467	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6728312	0.94[ASN][1000 genomes]
rs6736735	0.85[CEU][hapmap]
rs6738401	1.00[ASN][1000 genomes]
rs6751727	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755021	1.00[ASN][1000 genomes]
rs6756969	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760008	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs68115667	0.94[ASN][1000 genomes]
rs6875	0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs71429373	1.00[ASN][1000 genomes]
rs718159	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570009	0.94[ASN][1000 genomes]
rs7578638	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582298	1.00[ASN][1000 genomes]
rs7588227	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591374	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593290	0.94[ASN][1000 genomes]
rs7594928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595039	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9784011	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9808558	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9973490	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7599043	ADRA2B	cis	parietal	SCAN
rs7599043	TEKT4	cis	cerebellum	SCAN
rs7599043	LONRF2	cis	parietal	SCAN
rs7599043	INPP4A	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503400-98505800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:98503600-98509000	Weak transcription	Small Intestine	intestine
3	chr2:98503600-98522800	Weak transcription	HUVEC	blood vessel
4	chr2:98503800-98505800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:98503800-98508000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:98503800-98508200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:98503800-98508800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:98503800-98509000	Weak transcription	Stomach Mucosa	stomach
9	chr2:98503800-98509800	Weak transcription	NH-A	brain
10	chr2:98503800-98516400	Weak transcription	HMEC	breast
11	chr2:98503800-98517200	Weak transcription	HSMM	muscle
12	chr2:98503800-98522600	Weak transcription	Fetal Kidney	kidney
13	chr2:98503800-98522800	Weak transcription	K562	blood
14	chr2:98503800-98524800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:98503800-98528600	Weak transcription	NHDF-Ad	bronchial
16	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
17	chr2:98504000-98505800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:98504000-98505800	Weak transcription	A549	lung
19	chr2:98504000-98506400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:98504000-98506400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:98504000-98506400	Weak transcription	Aorta	Aorta
22	chr2:98504000-98506400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:98504000-98507400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:98504000-98507600	Weak transcription	Fetal Thymus	thymus
25	chr2:98504000-98507800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:98504000-98507800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:98504000-98507800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:98504000-98508400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:98504000-98508800	Weak transcription	Pancreas	Pancrea
30	chr2:98504000-98508800	Weak transcription	Right Ventricle	heart
31	chr2:98504000-98521800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:98504000-98521800	Weak transcription	Fetal Lung	lung
33	chr2:98504000-98522000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:98504000-98522200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:98504000-98522400	Weak transcription	Primary B cells from cord blood	blood
36	chr2:98504000-98522800	Weak transcription	Fetal Brain Female	brain
37	chr2:98504000-98523000	Weak transcription	Psoas Muscle	Psoas
38	chr2:98504000-98523600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:98504000-98528000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
41	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:98504200-98506400	Weak transcription	Lung	lung
45	chr2:98504200-98507000	Weak transcription	Colonic Mucosa	Colon
46	chr2:98504200-98507600	Weak transcription	NHEK	skin
47	chr2:98504200-98507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:98504200-98508000	Weak transcription	Brain Angular Gyrus	brain
49	chr2:98504200-98508800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:98504200-98517600	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links