Variant report

Variant	rs946054
Chromosome Location	chr9:103044015-103044016
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103037852..103042243-chr9:103042555..103047658,4	K562	blood:

Extended variants
information (count: 179 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10116798	0.80[EUR][1000 genomes]
rs10117150	0.80[EUR][1000 genomes]
rs10117799	0.93[ASN][1000 genomes]
rs10118398	0.83[ASN][1000 genomes]
rs10118701	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs10120244	0.82[ASN][1000 genomes]
rs10123866	0.93[ASN][1000 genomes]
rs10123913	0.93[ASN][1000 genomes]
rs10124133	0.83[ASN][1000 genomes]
rs10124893	0.91[ASN][1000 genomes]
rs10125785	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1014651	0.82[JPT][hapmap]
rs1014652	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10739796	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10760720	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10760724	0.92[ASN][1000 genomes]
rs10819737	0.93[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10819751	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10819759	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10819761	0.87[ASN][1000 genomes]
rs10819762	0.83[ASN][1000 genomes]
rs10819764	0.83[ASN][1000 genomes]
rs10819767	0.83[ASN][1000 genomes]
rs10989049	0.95[ASN][1000 genomes]
rs10989056	0.85[ASN][1000 genomes]
rs10989064	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10989067	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10989070	0.83[ASN][1000 genomes]
rs11789196	0.93[ASN][1000 genomes]
rs12336751	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12684939	0.84[ASN][1000 genomes]
rs13301295	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1338119	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1338121	0.86[ASN][1000 genomes]
rs1338123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338125	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338126	0.86[ASN][1000 genomes]
rs1361668	0.82[JPT][hapmap]
rs1415926	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1529192	0.89[CEU][hapmap]
rs1534726	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs1539297	0.82[JPT][hapmap]
rs1572607	0.82[JPT][hapmap]
rs1930243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1961367	0.85[ASN][1000 genomes]
rs1999877	0.82[JPT][hapmap]
rs2026999	0.83[ASN][1000 genomes]
rs2065997	0.85[ASN][1000 genomes]
rs2151131	1.00[CHB][hapmap]
rs2181579	0.82[JPT][hapmap]
rs2210498	0.83[ASN][1000 genomes]
rs2245216	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2417084	0.83[ASN][1000 genomes]
rs2417176	0.83[ASN][1000 genomes]
rs2476441	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2476442	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2485745	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2491095	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2491098	0.83[ASN][1000 genomes]
rs2761056	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2787361	0.92[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2787363	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2787365	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2787366	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs2787368	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787369	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787370	0.88[ASN][1000 genomes]
rs2787371	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2787372	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787373	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787374	0.85[ASN][1000 genomes]
rs2787375	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787376	0.86[ASN][1000 genomes]
rs2787377	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2787379	0.86[ASN][1000 genomes]
rs2787380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787381	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787382	0.86[ASN][1000 genomes]
rs2787383	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2787384	0.86[ASN][1000 genomes]
rs2787385	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787386	0.83[ASN][1000 genomes]
rs2787388	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2787390	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2787391	0.82[JPT][hapmap]
rs2787394	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2787395	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2787397	0.85[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2806682	0.93[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2806683	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2806684	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2806688	0.81[ASN][1000 genomes]
rs2806689	0.86[ASN][1000 genomes]
rs2806690	0.84[ASN][1000 genomes]
rs2806691	0.86[ASN][1000 genomes]
rs2806692	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2806693	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806695	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2806696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2806699	0.85[ASN][1000 genomes]
rs2806700	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2806702	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806703	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28464821	0.87[ASN][1000 genomes]
rs3813712	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3923501	0.95[ASN][1000 genomes]
rs4128230	0.91[ASN][1000 genomes]
rs4237194	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4237195	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs4237196	0.85[ASN][1000 genomes]
rs4446782	0.95[ASN][1000 genomes]
rs4517187	0.82[JPT][hapmap]
rs4742782	0.93[ASN][1000 genomes]
rs4742783	0.88[ASN][1000 genomes]
rs4742784	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4743392	0.95[ASN][1000 genomes]
rs4743393	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4743394	0.87[ASN][1000 genomes]
rs4743395	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4743396	0.83[ASN][1000 genomes]
rs5029342	0.93[ASN][1000 genomes]
rs5029343	0.95[ASN][1000 genomes]
rs59242794	0.87[ASN][1000 genomes]
rs6479001	0.89[CEU][hapmap]
rs6479002	0.89[CEU][hapmap]
rs6479008	0.90[ASN][1000 genomes]
rs6479009	0.95[ASN][1000 genomes]
rs6479011	0.84[ASN][1000 genomes]
rs6479013	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6479014	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7020988	0.95[ASN][1000 genomes]
rs7021310	0.85[ASN][1000 genomes]
rs7025891	0.83[ASN][1000 genomes]
rs7025938	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs7035619	0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs7036570	0.85[ASN][1000 genomes]
rs7048601	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7472	0.93[ASN][1000 genomes]
rs7846794	0.89[CEU][hapmap]
rs7847213	0.89[CEU][hapmap]
rs7849966	0.95[ASN][1000 genomes]
rs7852189	0.83[ASN][1000 genomes]
rs7854693	0.93[ASN][1000 genomes]
rs7859492	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7860513	0.85[ASN][1000 genomes]
rs7864494	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866850	0.85[ASN][1000 genomes]
rs7869985	0.85[ASN][1000 genomes]
rs7871702	0.85[ASN][1000 genomes]
rs7874900	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7875775	0.85[ASN][1000 genomes]
rs846752	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs846753	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs846756	0.89[CEU][hapmap]
rs846761	0.93[CEU][hapmap]
rs846762	0.82[JPT][hapmap]
rs846765	0.83[EUR][1000 genomes]
rs846768	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs846769	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs846770	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs860171	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs914711	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9299337	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9299338	0.83[ASN][1000 genomes]
rs9408995	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9408998	0.87[ASN][1000 genomes]
rs9409325	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs944710	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs959893	0.88[ASN][1000 genomes]
rs9695692	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9775014	0.89[ASN][1000 genomes]
rs9775182	0.95[ASN][1000 genomes]
rs9886877	0.81[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs946054	STX17	cis	Esophagus Mucosa	GTEx
rs946054	INVS	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102972600-103046600	Weak transcription	Psoas Muscle	Psoas
2	chr9:102973000-103053800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:102974000-103047600	Weak transcription	Fetal Brain Male	brain
4	chr9:102975800-103045800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:102976800-103047800	Weak transcription	Fetal Heart	heart
6	chr9:102979400-103054600	Weak transcription	NHEK	skin
7	chr9:102987400-103045800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:102987400-103054600	Weak transcription	Gastric	stomach
9	chr9:102989400-103047200	Weak transcription	GM12878-XiMat	blood
10	chr9:102994800-103046600	Weak transcription	Pancreas	Pancrea
11	chr9:102997800-103054400	Weak transcription	Colonic Mucosa	Colon
12	chr9:103003400-103046800	Weak transcription	HMEC	breast
13	chr9:103009400-103047600	Weak transcription	HUVEC	blood vessel
14	chr9:103013000-103047400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:103015000-103046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:103015400-103046400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:103015400-103046600	Weak transcription	Brain Substantia Nigra	brain
18	chr9:103015400-103046800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:103015600-103046600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:103016000-103044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:103016000-103047200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:103021800-103044400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:103021800-103044400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:103022000-103047800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:103023800-103046200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:103026200-103047600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:103027800-103046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:103027800-103046600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:103028000-103044800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:103028000-103046400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:103028200-103046200	Weak transcription	Fetal Kidney	kidney
32	chr9:103028400-103046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:103028600-103044600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:103028600-103046400	Weak transcription	Brain Germinal Matrix	brain
35	chr9:103029000-103053600	Weak transcription	Hela-S3	cervix
36	chr9:103029200-103046000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:103029200-103046600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr9:103029200-103047000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr9:103029200-103047600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:103029200-103054600	Weak transcription	Brain Angular Gyrus	brain
41	chr9:103029800-103046600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:103029800-103047400	Weak transcription	HepG2	liver
43	chr9:103031200-103046400	Weak transcription	Small Intestine	intestine
44	chr9:103034200-103047200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:103034800-103047400	Strong transcription	Primary T cells from cord blood	blood
46	chr9:103035000-103046000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:103035000-103047200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:103035600-103046200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr9:103035600-103046600	Weak transcription	Lung	lung
50	chr9:103035600-103046600	Weak transcription	Spleen	Spleen

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