Variant report

Variant	rs9656060
Chromosome Location	chr7:99106674-99106675
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	chr7:99104777..99107426-chr7:99112008..99113536,2	K562	blood:
2	chr7:99102115..99104059-chr7:99105392..99107094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196652	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10215765	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10264505	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268984	1.00[ASN][1000 genomes]
rs10273424	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10278040	0.97[AFR][1000 genomes]
rs10808111	0.86[EUR][1000 genomes]
rs10808112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	0.86[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	0.98[AMR][1000 genomes];0.95[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]
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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12538826	0.81[EUR][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243267	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[ASN][1000 genomes]
rs17161761	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[ASN][1000 genomes]
rs28419687	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627543	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[ASN][1000 genomes]
rs34257469	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34967184	1.00[ASN][1000 genomes]
rs35183025	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.86[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	0.94[AFR][1000 genomes];0.89[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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960810	1.00[ASN][1000 genomes]
rs704798	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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs9656060	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	chr7:99103800-99125600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99104000-99108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:99104000-99113000	Weak transcription	Aorta	Aorta
4	chr7:99104200-99108600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:99104200-99108600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:99104200-99109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:99104200-99110000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:99104200-99110000	Weak transcription	Esophagus	oesophagus
9	chr7:99104200-99110000	Weak transcription	HSMMtube	muscle
10	chr7:99104200-99112600	Weak transcription	Small Intestine	intestine
11	chr7:99104200-99113600	Weak transcription	Pancreas	Pancrea
12	chr7:99104200-99114000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:99104200-99118600	Weak transcription	Right Atrium	heart
14	chr7:99104200-99123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:99104400-99107600	Weak transcription	Lung	lung
16	chr7:99104600-99107800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:99104600-99109400	Weak transcription	Primary B cells from cord blood	blood
18	chr7:99104800-99106800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:99104800-99107000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:99104800-99107400	Weak transcription	Placenta	Placenta
21	chr7:99104800-99109000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:99105000-99107200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:99105000-99107400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:99105000-99107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:99105000-99107600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:99105000-99107600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:99105000-99108400	Weak transcription	Primary T cells from cord blood	blood
28	chr7:99105000-99108400	Weak transcription	Brain Anterior Caudate	brain
29	chr7:99105000-99108400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:99105000-99108400	Weak transcription	Thymus	Thymus
31	chr7:99105000-99108600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:99105000-99108600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:99105000-99108600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:99105000-99108600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:99105000-99108600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:99105000-99108600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:99105000-99108600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:99105000-99108600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:99105000-99108600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:99105000-99108600	Weak transcription	A549	lung
41	chr7:99105000-99108600	Weak transcription	HepG2	liver
42	chr7:99105000-99108600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:99105000-99109400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr7:99105000-99109600	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:99105000-99109600	Weak transcription	Fetal Lung	lung
46	chr7:99105000-99109600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:99105000-99109800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:99105000-99109800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:99105000-99109800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr7:99105000-99109800	Weak transcription	HMEC	breast

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