Variant report

Variant	rs10989169
Chromosome Location	chr9:103362008-103362009
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103360698..103363075-chr9:104159012..104161996,2	MCF-7	breast:
2	chr9:103358110..103359783-chr9:103360702..103363224,2	MCF-7	breast:
3	chr9:103361504..103363020-chr9:103366654..103368893,2	K562	blood:

Variant related genes	Relation type
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1000477	0.82[JPT][hapmap]
rs10465118	1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs10465147	0.82[JPT][hapmap]
rs10465148	0.82[JPT][hapmap]
rs10465149	0.82[JPT][hapmap]
rs10512270	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10512271	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10819773	0.81[JPT][hapmap]
rs10819776	0.82[JPT][hapmap]
rs10819782	0.82[JPT][hapmap]
rs10819785	0.82[JPT][hapmap]
rs10819787	0.82[JPT][hapmap]
rs10819788	0.82[JPT][hapmap]
rs10819789	0.82[JPT][hapmap]
rs10819795	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10989078	0.82[JPT][hapmap]
rs10989081	0.82[JPT][hapmap]
rs10989082	0.82[JPT][hapmap]
rs10989085	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989094	0.82[JPT][hapmap]
rs10989097	0.82[JPT][hapmap]
rs10989103	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989105	0.82[JPT][hapmap]
rs10989107	1.00[CEU][hapmap]
rs10989111	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10989112	0.82[JPT][hapmap]
rs10989113	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989114	1.00[CEU][hapmap]
rs10989115	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989120	0.81[JPT][hapmap]
rs10989123	0.82[JPT][hapmap]
rs10989127	0.82[JPT][hapmap]
rs10989130	0.82[JPT][hapmap]
rs10989131	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989144	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10989145	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10989146	0.88[JPT][hapmap]
rs10989147	1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap]
rs10989150	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10989152	0.91[JPT][hapmap]
rs10989153	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs10989154	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap]
rs10989156	0.92[JPT][hapmap]
rs10989161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989163	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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989164	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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989170	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989173	0.97[ASN][1000 genomes]
rs10989174	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11793014	0.82[JPT][hapmap]
rs12004257	0.82[JPT][hapmap]
rs12056981	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12235981	0.92[JPT][hapmap]
rs12236071	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap]
rs12236970	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs12237481	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12238560	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12683122	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]
rs12683548	1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12683889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12684438	0.82[JPT][hapmap]
rs12684454	0.82[JPT][hapmap]
rs12685564	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1332598	0.82[JPT][hapmap]
rs16919174	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs16919204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1930246	0.82[JPT][hapmap]
rs1931140	0.92[JPT][hapmap]
rs2026423	0.82[JPT][hapmap]
rs2069236	0.82[JPT][hapmap]
rs2151106	0.82[JPT][hapmap]
rs2183989	0.82[JPT][hapmap]
rs2183990	0.82[JPT][hapmap]
rs2183991	0.82[JPT][hapmap]
rs2274881	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs2274882	0.82[JPT][hapmap]
rs28623148	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4454331	0.97[ASN][1000 genomes]
rs55757829	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56290508	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56354846	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7021028	0.92[JPT][hapmap]
rs7028822	0.82[JPT][hapmap]
rs7029001	0.82[JPT][hapmap]
rs7042669	0.82[JPT][hapmap]
rs7046659	0.82[JPT][hapmap]
rs72735197	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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv893624	chr9:103351931-103416553	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103360800-103362200	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:103361200-103372800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:103361400-103362200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:103361600-103362200	Enhancers	Primary T cells from cord blood	blood
5	chr9:103361600-103362800	Weak transcription	HSMMtube	muscle
6	chr9:103361600-103363800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr9:103361600-103364400	Enhancers	Fetal Muscle Leg	muscle
8	chr9:103361800-103362200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:103361800-103362200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr9:103361800-103362200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:103361800-103362200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr9:103361800-103362200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr9:103361800-103362200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr9:103361800-103362200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:103361800-103362200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:103361800-103362800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:103361800-103362800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:103361800-103362800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:103361800-103362800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:103361800-103362800	Weak transcription	HSMM	muscle
21	chr9:103361800-103363000	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:103361800-103363000	Weak transcription	Psoas Muscle	Psoas
23	chr9:103361800-103363200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:103361800-103363200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:103361800-103363200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:103361800-103363600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:103361800-103363600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:103361800-103363600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:103361800-103363600	Enhancers	NHEK	skin
30	chr9:103361800-103363800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:103361800-103363800	Weak transcription	Lung	lung
32	chr9:103361800-103364600	Weak transcription	Fetal Brain Male	brain
33	chr9:103361800-103364600	Weak transcription	Right Atrium	heart
34	chr9:103361800-103364800	Weak transcription	Brain Anterior Caudate	brain
35	chr9:103361800-103364800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:103361800-103367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:103362000-103362800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:103362000-103362800	Weak transcription	K562	blood
39	chr9:103362000-103363000	Weak transcription	HepG2	liver
40	chr9:103362000-103363600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:103362000-103363600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:103362000-103363800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr9:103362000-103364600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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