Variant report

Variant	rs10235235
Chromosome Location	chr7:99075831-99075832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99068902..99074011-chr7:99074957..99079531,8	MCF-7	breast:
2	chr7:99061928..99063883-chr7:99075235..99077216,3	MCF-7	breast:
3	chr7:99041079..99042871-chr7:99074041..99075977,2	K562	blood:
4	chr7:99069496..99072667-chr7:99072993..99076843,7	MCF-7	breast:
5	chr7:99074811..99076885-chr7:99166802..99169716,2	K562	blood:
6	chr7:99075466..99078663-chr7:99096461..99098566,3	K562	blood:
7	chr7:99075804..99077821-chr7:99161750..99163341,2	K562	blood:

Variant related genes	Relation type
ENSG00000160917	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000228335	Chromatin interaction
ENSG00000197343	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000198556	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10215765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10240199	0.86[EUR][1000 genomes]
rs10264505	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265385	0.86[EUR][1000 genomes]
rs10268984	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10273424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10808111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808112	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761528	1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11972017	1.00[CHB][hapmap]
rs11973173	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974593	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11974885	1.00[CHB][hapmap]
rs11977673	1.00[CHD][hapmap]
rs11978345	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11978582	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs12531852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12533251	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17161761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[ASN][1000 genomes]
rs28419687	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627543	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28862110	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34257469	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34967184	1.00[ASN][1000 genomes]
rs35183025	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs61740607	1.00[ASN][1000 genomes]
rs66478766	1.00[ASN][1000 genomes]
rs66509940	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66568021	1.00[ASN][1000 genomes]
rs66674233	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs67934834	1.00[ASN][1000 genomes]
rs6947826	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960805	1.00[CHB][hapmap]
rs6960810	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6961579	1.00[CHB][hapmap]
rs704798	1.00[ASN][1000 genomes]
rs73157600	1.00[ASN][1000 genomes]
rs73157601	1.00[ASN][1000 genomes]
rs73157602	1.00[ASN][1000 genomes]
rs73159506	1.00[ASN][1000 genomes]
rs73159509	1.00[ASN][1000 genomes]
rs73159522	1.00[ASN][1000 genomes]
rs73163167	1.00[ASN][1000 genomes]
rs73163169	1.00[ASN][1000 genomes]
rs740160	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs9632722	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656060	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10235235	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99071200-99076200	Weak transcription	Aorta	Aorta
2	chr7:99071200-99077600	Weak transcription	Ovary	ovary
3	chr7:99071200-99091000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:99071200-99091600	Weak transcription	Small Intestine	intestine
5	chr7:99071400-99076800	Weak transcription	NHEK	skin
6	chr7:99071400-99077000	Weak transcription	Fetal Lung	lung
7	chr7:99071400-99081600	Weak transcription	Right Ventricle	heart
8	chr7:99071400-99090400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:99071400-99090600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:99071400-99090600	Weak transcription	Right Atrium	heart
11	chr7:99071400-99096200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:99071600-99076000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:99071600-99090400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:99071600-99091200	Weak transcription	Fetal Heart	heart
15	chr7:99071800-99076000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:99071800-99076000	Weak transcription	Left Ventricle	heart
17	chr7:99071800-99076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:99071800-99076200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:99071800-99076200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:99071800-99077200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:99071800-99077200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:99071800-99079600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:99071800-99080200	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:99071800-99081800	Weak transcription	Pancreas	Pancrea
25	chr7:99071800-99084400	Weak transcription	Fetal Brain Male	brain
26	chr7:99071800-99088600	Weak transcription	Brain Substantia Nigra	brain
27	chr7:99071800-99090400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:99071800-99090400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:99071800-99090400	Weak transcription	Psoas Muscle	Psoas
30	chr7:99071800-99090600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:99071800-99091600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:99072000-99086400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:99072400-99076800	Weak transcription	HMEC	breast
34	chr7:99072400-99077400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:99072400-99077600	Weak transcription	HUVEC	blood vessel
36	chr7:99072400-99078600	Strong transcription	Fetal Intestine Small	intestine
37	chr7:99072400-99083600	Weak transcription	Stomach Mucosa	stomach
38	chr7:99072600-99076200	Strong transcription	Fetal Stomach	stomach
39	chr7:99072600-99091200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:99073000-99080000	Strong transcription	Brain Germinal Matrix	brain
41	chr7:99073200-99082200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:99073600-99076000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:99073600-99078400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:99073600-99080200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:99073600-99080600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:99073600-99084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:99073800-99076000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:99073800-99076000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr7:99073800-99077000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr7:99073800-99078400	Strong transcription	Fetal Intestine Large	intestine

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