Variant report

Variant	rs698475
Chromosome Location	chr9:110099538-110099539
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	chr9:108672760..108675101-chr9:110098994..110101048,2	MCF-7	breast:
2	chr9:110044860..110047881-chr9:110095955..110100656,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10113916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119641	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10122970	0.87[ASN][1000 genomes]
rs10481632	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10521083	0.84[CHB][hapmap];0.91[CHD][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10732368	0.84[CHB][hapmap]
rs10739232	0.87[CHB][hapmap]
rs10739234	0.84[CHB][hapmap]
rs10739236	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739238	0.84[CHB][hapmap]
rs10759219	0.89[CHB][hapmap]
rs10759222	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs10759225	0.83[CHD][hapmap]
rs10816477	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816480	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816485	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816490	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978767	0.94[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs10978769	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10978770	0.89[CHB][hapmap]
rs10978775	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978776	0.87[ASN][1000 genomes]
rs10978777	0.87[ASN][1000 genomes]
rs10978791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342066	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12345455	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12551936	0.84[CEU][hapmap]
rs12555417	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1323809	0.83[CHD][hapmap]
rs1535765	0.84[CHB][hapmap]
rs1535766	0.89[CHB][hapmap]
rs1805329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805332	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs1805334	0.84[CHB][hapmap];0.91[CHD][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1805335	0.85[CHD][hapmap]
rs1886134	0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs2005143	0.82[ASN][1000 genomes]
rs2147072	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs2417776	0.87[ASN][1000 genomes]
rs2417784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417785	0.84[CHB][hapmap]
rs28534368	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28769087	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28848858	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4278207	0.84[CHB][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs4481670	0.83[CHB][hapmap]
rs4978404	0.83[EUR][1000 genomes]
rs4978406	0.84[EUR][1000 genomes]
rs4978849	0.83[CHB][hapmap]
rs61701375	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7025563	0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs7029997	0.84[CHB][hapmap]
rs7030169	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7030555	0.80[EUR][1000 genomes]
rs7031906	0.84[CHB][hapmap]
rs7035611	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs7036284	0.87[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap]
rs7040217	0.96[ASN][1000 genomes]
rs7041137	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap];0.91[CHD][hapmap];0.84[EUR][1000 genomes]
rs7046950	0.84[CHB][hapmap]
rs7852295	0.89[CHB][hapmap]
rs7866312	0.89[CHB][hapmap]
rs7866353	0.89[CHB][hapmap]
rs7866797	0.89[CHB][hapmap]
rs7867544	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs7873745	0.86[ASN][1000 genomes]
rs817836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817838	1.00[ASN][1000 genomes]
rs817839	1.00[ASN][1000 genomes]
rs817840	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs817841	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs817843	1.00[ASN][1000 genomes]
rs817844	1.00[ASN][1000 genomes]
rs817845	1.00[ASN][1000 genomes]
rs817847	0.93[ASN][1000 genomes]
rs817849	0.88[ASN][1000 genomes]
rs817851	0.88[ASN][1000 genomes]
rs942291	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs942292	0.88[CHD][hapmap]
rs942293	0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs9632893	0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969728	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs698475	TXN	cis	parietal	SCAN
rs698475	OR13C8	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
3	chr9:110087600-110103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:110088400-110101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:110088600-110101600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:110090400-110101800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:110091000-110103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:110092000-110101800	Strong transcription	Primary T cells from cord blood	blood
9	chr9:110093000-110103400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:110093200-110101800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:110093200-110103200	Strong transcription	A549	lung
12	chr9:110093200-110103400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr9:110094600-110101600	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr9:110094800-110100800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:110094800-110101800	Strong transcription	Fetal Intestine Small	intestine
16	chr9:110095000-110104600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:110095400-110099600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:110095400-110101600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:110095600-110103400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:110096000-110100400	Weak transcription	Fetal Heart	heart
21	chr9:110096000-110103400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr9:110096200-110103200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:110096200-110103400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:110096600-110103200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:110096600-110103400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr9:110096600-110103400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:110096800-110100600	Weak transcription	Fetal Brain Female	brain
28	chr9:110096800-110101000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:110096800-110102600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:110096800-110103400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:110096800-110103400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:110096800-110107200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:110097000-110100000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:110097000-110100400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr9:110097000-110100400	Weak transcription	Ovary	ovary
36	chr9:110097000-110100400	Weak transcription	Thymus	Thymus
37	chr9:110097000-110100600	Weak transcription	Brain Germinal Matrix	brain
38	chr9:110097000-110100600	Weak transcription	GM12878-XiMat	blood
39	chr9:110097000-110100800	Weak transcription	Fetal Lung	lung
40	chr9:110097000-110102600	Weak transcription	Colonic Mucosa	Colon
41	chr9:110097000-110103200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:110097000-110103200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:110097000-110103400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:110097000-110103400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:110097000-110103400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:110097000-110103400	Weak transcription	Gastric	stomach
47	chr9:110097000-110103600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:110097000-110103600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:110097000-110104600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:110097000-110107200	Weak transcription	Fetal Kidney	kidney

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