Variant report

Variant	rs28627543
Chromosome Location	chr7:99059950-99059951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99058626..99061250-chr7:99076948..99079594,2	K562	blood:
2	chr7:99055792..99058380-chr7:99059202..99061148,2	MCF-7	breast:
3	chr7:99057427..99060113-chr7:99097887..99100636,2	K562	blood:
4	chr7:99055033..99067556-chr7:99095016..99105645,21	K562	blood:
5	chr7:99058374..99059981-chr7:99097679..99100628,2	MCF-7	breast:
6	chr7:99007269..99009205-chr7:99058762..99060773,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106245	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000196652	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10215765	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10264505	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268984	1.00[ASN][1000 genomes]
rs10273424	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10278040	0.86[AFR][1000 genomes]
rs10808111	0.91[EUR][1000 genomes]
rs10808112	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761528	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11973173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974593	1.00[ASN][1000 genomes]
rs11978345	1.00[ASN][1000 genomes]
rs11978582	1.00[ASN][1000 genomes]
rs11980143	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[ASN][1000 genomes]
rs12533251	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12538826	0.86[EUR][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243267	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[ASN][1000 genomes]
rs17161761	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[ASN][1000 genomes]
rs28419687	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[ASN][1000 genomes]
rs34257469	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183025	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.91[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	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[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	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960810	1.00[ASN][1000 genomes]
rs704798	1.00[ASN][1000 genomes]
rs73157596	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	1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs9632722	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656060	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	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
rs28627543	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99038000-99061600	Strong transcription	Fetal Stomach	stomach
2	chr7:99038200-99061800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:99038200-99061800	Strong transcription	Fetal Intestine Small	intestine
4	chr7:99038200-99062000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:99038200-99062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:99038200-99062400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:99038400-99062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:99038600-99062400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:99039200-99061600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:99039600-99062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:99040000-99060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:99040400-99060800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr7:99040400-99062000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:99040800-99062000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:99044200-99060400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:99046600-99062800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:99056400-99060600	Strong transcription	Fetal Muscle Leg	muscle
18	chr7:99056400-99060600	Weak transcription	HUVEC	blood vessel
19	chr7:99056400-99061600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr7:99056600-99060400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:99057000-99062400	Weak transcription	Fetal Kidney	kidney
22	chr7:99057000-99062800	Weak transcription	HSMMtube	muscle
23	chr7:99057200-99060400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr7:99057200-99062400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:99057200-99062600	Weak transcription	Stomach Mucosa	stomach
26	chr7:99057400-99060200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:99057400-99061800	Genic enhancers	HepG2	liver
28	chr7:99057400-99063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:99057600-99060400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:99057600-99060400	Weak transcription	Primary B cells from cord blood	blood
31	chr7:99057600-99062600	Weak transcription	Small Intestine	intestine
32	chr7:99057800-99060400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:99057800-99060400	Weak transcription	Osteobl	bone
34	chr7:99057800-99061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:99058000-99060400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:99058000-99060600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:99058000-99061400	Weak transcription	NHDF-Ad	bronchial
38	chr7:99058000-99061600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:99058000-99062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr7:99058000-99062600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:99058200-99060400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:99058200-99060400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:99058200-99060400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr7:99058200-99060400	Weak transcription	Colon Smooth Muscle	Colon
45	chr7:99058200-99060400	Weak transcription	NH-A	brain
46	chr7:99058200-99061400	Genic enhancers	K562	blood
47	chr7:99058200-99062000	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr7:99058400-99060400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:99058400-99060600	Weak transcription	Liver	Liver
50	chr7:99058400-99061400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links