Variant report

Variant	rs12535424
Chromosome Location	chr7:99053816-99053817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99005077..99006635-chr7:99051986..99054907,2	K562	blood:
2	chr7:99034720..99038160-chr7:99048984..99054018,5	MCF-7	breast:
3	chr7:99048592..99050764-chr7:99052793..99054929,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160917	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10215765	0.81[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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	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]
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];0.86[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];0.84[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];0.91[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	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761528	1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.84[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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.84[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	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]
rs11980143	1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs11984190	1.00[YRI][hapmap]
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]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.84[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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][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	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.83[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183025	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	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.84[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	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]
rs67279166	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs67934834	1.00[ASN][1000 genomes]
rs6947826	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]
rs6947941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.84[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]
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[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: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
rs12535424	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	chr7:99038000-99054600	Weak transcription	Stomach Mucosa	stomach
2	chr7:99038000-99061600	Strong transcription	Fetal Stomach	stomach
3	chr7:99038200-99056200	Weak transcription	Fetal Heart	heart
4	chr7:99038200-99061800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:99038200-99061800	Strong transcription	Fetal Intestine Small	intestine
6	chr7:99038200-99062000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:99038200-99062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:99038200-99062400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:99038400-99062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:99038600-99058000	Strong transcription	NHEK	skin
11	chr7:99038600-99058600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:99038600-99062400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:99038800-99058000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:99039000-99055000	Strong transcription	Placenta	Placenta
15	chr7:99039000-99059000	Strong transcription	Fetal Intestine Large	intestine
16	chr7:99039200-99054000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:99039200-99058200	Strong transcription	Dnd41	blood
20	chr7:99039200-99061600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:99039400-99059600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:99039600-99058000	Strong transcription	HMEC	breast
23	chr7:99039600-99062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:99039800-99054400	Weak transcription	Right Atrium	heart
25	chr7:99040000-99058400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:99040000-99058600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:99040000-99059000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr7:99040000-99060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:99040200-99058200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:99040200-99059400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:99040200-99059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:99040400-99058200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr7:99040400-99058400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:99040400-99058400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:99040400-99058600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr7:99040400-99058600	Strong transcription	Fetal Lung	lung
37	chr7:99040400-99059000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:99040400-99059600	Strong transcription	Primary T cells from cord blood	blood
39	chr7:99040400-99060800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr7:99040400-99062000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:99040600-99057200	Strong transcription	Ovary	ovary
42	chr7:99040600-99058400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:99040800-99055000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:99040800-99062000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr7:99041000-99057600	Strong transcription	Fetal Brain Female	brain
46	chr7:99041000-99058400	Strong transcription	Liver	Liver
47	chr7:99041000-99058600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:99041000-99058600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr7:99041200-99058600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:99041400-99058400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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