Variant report

Variant	rs10229408
Chromosome Location	chr7:66627394-66627395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10155890	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10155918	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10155972	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10155983	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10156209	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10228308	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10231586	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10233388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10233967	0.81[AFR][1000 genomes]
rs10234659	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10235588	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10238245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10242790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10243217	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10246747	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10247133	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10249781	0.81[AFR][1000 genomes]
rs10250113	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10250487	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10251763	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10252143	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10253339	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10256139	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10257949	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10262150	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10267300	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10267317	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10268701	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10270292	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10271374	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10272347	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10272591	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10273692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10274725	0.81[AFR][1000 genomes]
rs10280559	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10280699	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11760347	0.81[EUR][1000 genomes]
rs11761100	0.81[EUR][1000 genomes]
rs11766203	0.83[AMR][1000 genomes]
rs11772455	0.81[AMR][1000 genomes]
rs11773274	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11773730	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12154409	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12154419	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12154846	0.81[AFR][1000 genomes]
rs12155044	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12155047	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12155051	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13222146	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13225639	0.81[AFR][1000 genomes]
rs17137288	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17139656	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17144722	0.86[CEU][hapmap];0.82[GIH][hapmap]
rs17180957	0.90[JPT][hapmap]
rs1815098	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1829931	0.81[AFR][1000 genomes]
rs1880278	0.81[AFR][1000 genomes]
rs1965479	0.84[AFR][1000 genomes]
rs2421404	1.00[CHB][hapmap]
rs2421419	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2690147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2690170	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28366417	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844097	1.00[CEU][hapmap]
rs2844157	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2844170	0.81[AFR][1000 genomes]
rs28534521	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28620117	0.81[AFR][1000 genomes]
rs28651697	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28715521	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28855791	0.81[AMR][1000 genomes]
rs28888421	0.81[AFR][1000 genomes]
rs3015884	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3107871	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34145691	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34317556	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34344363	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34654147	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35048638	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35408354	0.81[AFR][1000 genomes]
rs35877378	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs36108108	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3962076	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3980767	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4101640	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4295533	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4551224	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4552791	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4559131	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4618581	0.85[AMR][1000 genomes]
rs4621684	0.83[AMR][1000 genomes]
rs4717353	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718463	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718464	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4718469	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4718470	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718471	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718475	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6460322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66734104	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs67855845	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6950170	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6951192	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6966142	0.81[AFR][1000 genomes]
rs6978789	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs71535637	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71535638	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71563178	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71563180	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73140602	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73142604	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7780458	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7783513	0.81[AFR][1000 genomes]
rs7796133	0.81[AFR][1000 genomes]
rs7804802	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9654771	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9654851	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9654853	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9654854	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9690121	0.81[AFR][1000 genomes]
rs9690145	0.83[AFR][1000 genomes]
rs9690291	0.81[AFR][1000 genomes]
rs9690839	0.81[AFR][1000 genomes]
rs9692120	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	esv1802655	chr7:66576034-66634666	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	esv1816643	chr7:66576034-66634666	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv1840497	chr7:66576034-66634666	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	esv1851064	chr7:66576034-66634666	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	esv1850306	chr7:66601324-66632583	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
10	esv1832033	chr7:66601324-66637001	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
11	esv1822512	chr7:66613751-66637001	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
12	esv1826252	chr7:66613751-66637001	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
13	esv1810114	chr7:66621964-66636410	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
14	esv2422035	chr7:66621964-66676630	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10229408	ZNF117	cis	parietal	SCAN
rs10229408	TYW1	cis	Heart Left Ventricle	GTEx
rs10229408	TYW1	cis	Muscle Skeletal	GTEx
rs10229408	ASL	cis	cerebellum	SCAN
rs10229408	TYW1	Cis_1M	lymphoblastoid	RTeQTL
rs10229408	TYW1	cis	Esophagus Mucosa	GTEx
rs10229408	TYW1	cis	lymphoblastoid	seeQTL
rs10229408	TYW1	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66595000-66627400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:66608800-66628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:66608800-66632600	Weak transcription	Ovary	ovary
4	chr7:66612400-66627600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:66614200-66628000	Weak transcription	K562	blood
6	chr7:66617200-66628200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:66617200-66628400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr7:66617400-66627400	Weak transcription	Primary T cells from cord blood	blood
9	chr7:66619400-66627600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr7:66619600-66628000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:66620600-66631000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:66620800-66628400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:66621000-66628200	Weak transcription	Thymus	Thymus
14	chr7:66621400-66628200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:66621400-66631400	Weak transcription	Adipose Nuclei	Adipose
16	chr7:66621600-66628400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:66621600-66672000	Weak transcription	Fetal Intestine Large	intestine
18	chr7:66621800-66628200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr7:66623400-66627600	Weak transcription	Fetal Intestine Small	intestine
20	chr7:66625200-66627800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:66626200-66627400	Enhancers	Hela-S3	cervix
22	chr7:66626800-66628200	Enhancers	Dnd41	blood
23	chr7:66626800-66629000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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