Variant report

Variant	rs10989064
Chromosome Location	chr9:103111965-103111966
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	chr9:103075126..103077245-chr9:103111933..103114024,2	MCF-7	breast:
2	chr9:103108889..103112022-chr9:103112659..103116565,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10117799	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118398	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118701	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10120244	0.98[ASN][1000 genomes]
rs10123866	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123913	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10124133	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124893	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10125785	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1014652	0.84[CHD][hapmap]
rs10739796	0.85[JPT][hapmap]
rs10760724	0.85[ASN][1000 genomes]
rs10819751	0.85[ASN][1000 genomes]
rs10819759	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[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819761	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819764	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819767	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989049	0.88[ASN][1000 genomes]
rs10989056	0.92[ASN][1000 genomes]
rs10989067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989070	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789196	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12336751	0.85[JPT][hapmap]
rs12684939	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1338121	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs1338123	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1338124	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1338125	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1338126	0.86[CHB][hapmap]
rs1415926	0.85[JPT][hapmap]
rs1572607	0.84[CHD][hapmap]
rs1930243	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1930244	0.90[ASN][1000 genomes]
rs1961367	0.98[ASN][1000 genomes]
rs1999877	0.83[CHD][hapmap]
rs2026999	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065997	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs2151131	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2210498	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245216	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2417084	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417176	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476441	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2485745	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2787363	0.85[JPT][hapmap]
rs2787364	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2787365	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2787368	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2787369	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2787371	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2787372	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs2787373	0.87[ASN][1000 genomes]
rs2787374	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs2787375	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2787377	0.88[ASN][1000 genomes]
rs2787379	0.86[CHB][hapmap]
rs2787380	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2787381	0.83[ASN][1000 genomes]
rs2787382	0.86[CHB][hapmap]
rs2787383	0.85[ASN][1000 genomes]
rs2787384	0.86[CHB][hapmap]
rs2787385	0.83[ASN][1000 genomes]
rs2787388	0.85[ASN][1000 genomes]
rs2787390	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs2787395	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2787396	0.85[JPT][hapmap]
rs2787397	0.91[CHD][hapmap];0.85[JPT][hapmap]
rs2806681	0.83[CHD][hapmap]
rs2806687	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2806691	0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2806692	0.85[ASN][1000 genomes]
rs2806693	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2806694	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2806695	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2806696	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2806699	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs2806700	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs2806702	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2806703	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28464821	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813712	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3923501	0.88[ASN][1000 genomes]
rs4128230	0.92[ASN][1000 genomes]
rs4237194	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4237195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237196	0.98[ASN][1000 genomes]
rs4446782	0.88[ASN][1000 genomes]
rs4742782	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742783	0.95[ASN][1000 genomes]
rs4742784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743392	0.88[ASN][1000 genomes]
rs4743393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743394	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743396	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5029342	0.86[CEU][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5029343	0.88[ASN][1000 genomes]
rs59242794	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479008	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479009	0.88[ASN][1000 genomes]
rs6479013	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs6479014	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7020988	0.88[ASN][1000 genomes]
rs7021310	0.98[ASN][1000 genomes]
rs7025891	0.97[ASN][1000 genomes]
rs7025938	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7035619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036570	0.98[ASN][1000 genomes]
rs7047694	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7048601	0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7472	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7849966	0.88[ASN][1000 genomes]
rs7852189	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854693	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7860513	0.98[ASN][1000 genomes]
rs7864494	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7866850	0.98[ASN][1000 genomes]
rs7869985	0.98[ASN][1000 genomes]
rs7871702	0.98[ASN][1000 genomes]
rs7874710	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7874900	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7875775	0.98[ASN][1000 genomes]
rs846752	0.85[JPT][hapmap]
rs846753	0.84[CHD][hapmap]
rs846766	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs846770	0.85[JPT][hapmap]
rs860171	0.85[JPT][hapmap]
rs914711	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9299338	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944710	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs946054	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs959893	0.95[ASN][1000 genomes]
rs9775014	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9775182	0.88[ASN][1000 genomes]
rs9886877	0.84[CHD][hapmap]

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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10989064	INVS	cis	multi-tissue	Pritchard
rs10989064	TEX10	cis	cerebellum	SCAN
rs10989064	TEX10	cis	Skin Sun Exposed Lower leg	GTEx
rs10989064	TEX10	cis	parietal	SCAN
rs10989064	LPPR1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
2	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
4	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
5	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
7	chr9:103072200-103113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:103074000-103113200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:103078400-103112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:103083800-103113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:103088400-103112000	Weak transcription	Brain Germinal Matrix	brain
12	chr9:103088600-103112400	Weak transcription	Brain Angular Gyrus	brain
13	chr9:103088600-103113000	Weak transcription	Fetal Brain Female	brain
14	chr9:103088600-103114400	Weak transcription	Lung	lung
15	chr9:103088800-103112400	Weak transcription	Psoas Muscle	Psoas
16	chr9:103088800-103113400	Weak transcription	Fetal Intestine Small	intestine
17	chr9:103088800-103114400	Weak transcription	Gastric	stomach
18	chr9:103089400-103112800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:103091200-103113200	Weak transcription	Liver	Liver
20	chr9:103092400-103112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:103092400-103113800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:103092600-103113800	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:103100800-103112600	Weak transcription	Aorta	Aorta
24	chr9:103100800-103113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:103101000-103113800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:103101400-103113200	Weak transcription	Fetal Stomach	stomach
27	chr9:103102000-103114000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:103104600-103113800	Weak transcription	Right Ventricle	heart
29	chr9:103104800-103112600	Weak transcription	Fetal Heart	heart
30	chr9:103105000-103112600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:103105400-103114000	Weak transcription	Brain Substantia Nigra	brain
32	chr9:103107000-103113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:103107200-103112400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:103108000-103112400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:103108000-103113800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:103108600-103112600	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:103108600-103114000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:103109200-103112000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:103109200-103112400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:103109200-103112400	Weak transcription	NHLF	lung
41	chr9:103109200-103113200	Weak transcription	Fetal Lung	lung
42	chr9:103109200-103113400	Weak transcription	Adipose Nuclei	Adipose
43	chr9:103109400-103112000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr9:103109400-103112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:103109400-103112000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:103109400-103112000	Weak transcription	Fetal Kidney	kidney
47	chr9:103109400-103112200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr9:103109400-103112400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:103109400-103112600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:103109400-103113000	Weak transcription	Brain Anterior Caudate	brain

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