Variant report

Variant	rs17136090
Chromosome Location	chr7:102475673-102475674
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	chr7:102474929..102477472-chr7:102495351..102498066,2	K562	blood:

Variant related genes	Relation type
ENSG00000238324	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10228495	0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10241865	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10242028	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10250490	0.84[ASN][1000 genomes]
rs10257317	0.86[ASN][1000 genomes]
rs10257543	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10271157	0.88[ASN][1000 genomes]
rs10271184	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10273725	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10279449	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10487283	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10499952	0.85[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10808120	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs10953374	0.85[ASN][1000 genomes]
rs1100044	0.81[EUR][1000 genomes]
rs1100046	0.82[ASN][1000 genomes]
rs11514917	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs11970869	0.82[EUR][1000 genomes]
rs11972019	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11972261	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs11972644	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11973870	0.85[EUR][1000 genomes]
rs11976237	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs11978670	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11978768	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11978799	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11980643	0.82[EUR][1000 genomes]
rs11981980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11983456	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11983521	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs12056296	0.81[EUR][1000 genomes]
rs12533386	0.81[EUR][1000 genomes]
rs12537977	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12538955	0.96[EUR][1000 genomes]
rs12540384	0.82[EUR][1000 genomes]
rs12666764	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12667218	0.85[EUR][1000 genomes]
rs12668434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669668	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13233521	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs13242493	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1541519	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1608651	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs17136137	0.82[EUR][1000 genomes]
rs2009503	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2159022	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2190673	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411056	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411059	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28856331	0.84[ASN][1000 genomes]
rs2908412	1.00[CEU][hapmap]
rs3779029	0.85[EUR][1000 genomes]
rs41501847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4296965	0.82[ASN][1000 genomes]
rs4620204	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4729860	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs56269620	0.95[ASN][1000 genomes]
rs56894117	0.85[EUR][1000 genomes]
rs56921864	0.82[EUR][1000 genomes]
rs57253646	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57350619	0.85[EUR][1000 genomes]
rs57368671	0.81[EUR][1000 genomes]
rs57545514	0.82[EUR][1000 genomes]
rs57776797	0.85[EUR][1000 genomes]
rs58191643	0.82[EUR][1000 genomes]
rs58680618	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58814323	0.99[EUR][1000 genomes]
rs58919995	0.96[EUR][1000 genomes]
rs59278165	0.82[EUR][1000 genomes]
rs59544295	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59709436	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60524601	0.85[EUR][1000 genomes]
rs60599650	0.85[EUR][1000 genomes]
rs61679881	0.82[EUR][1000 genomes]
rs6465876	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6465877	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6465878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6465879	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6465880	0.88[ASN][1000 genomes]
rs6465882	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs6465885	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs6942855	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6945369	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6946773	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6947403	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6949150	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6949391	0.86[ASN][1000 genomes]
rs6951288	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6953980	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956781	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6957434	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6957771	0.81[EUR][1000 genomes]
rs6960428	0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6967389	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6968713	0.85[CEU][hapmap]
rs6969054	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6975388	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6975451	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6976005	0.85[EUR][1000 genomes]
rs6977145	0.82[EUR][1000 genomes]
rs73406250	0.95[EUR][1000 genomes]
rs73406284	0.82[EUR][1000 genomes]
rs73406302	0.82[EUR][1000 genomes]
rs73408204	0.82[EUR][1000 genomes]
rs7778418	0.98[CHD][hapmap];0.90[JPT][hapmap]
rs7779145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779618	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7780981	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];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7782908	0.95[JPT][hapmap]
rs7785272	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs7789252	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7794668	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7796335	0.82[EUR][1000 genomes]
rs7800387	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7800548	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7804322	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs847646	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs847647	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs847648	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs847649	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs847652	0.85[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs847656	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs847658	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs865865	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs869332	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs9690210	0.84[EUR][1000 genomes]
rs9718453	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv608059	chr7:102470455-102504773	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17136090	LRWD1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr7:102447400-102477200	Weak transcription	Psoas Muscle	Psoas
3	chr7:102448000-102479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:102452000-102480000	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:102459800-102481800	Weak transcription	Brain Substantia Nigra	brain
7	chr7:102460400-102477000	Weak transcription	Stomach Mucosa	stomach
8	chr7:102460400-102480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:102460800-102480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:102468000-102484600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:102468200-102481000	Weak transcription	Brain Germinal Matrix	brain
12	chr7:102469800-102477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:102469800-102478400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:102469800-102478800	Weak transcription	Primary B cells from cord blood	blood
15	chr7:102470000-102477600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:102470000-102478000	Weak transcription	HepG2	liver
17	chr7:102470000-102479000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:102470000-102490200	Weak transcription	Gastric	stomach
19	chr7:102470000-102516400	Weak transcription	Pancreas	Pancrea
20	chr7:102470200-102476800	Weak transcription	Fetal Heart	heart
21	chr7:102470200-102477000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:102470200-102478400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr7:102470200-102481800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:102470400-102476800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:102470400-102477200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:102470400-102477600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:102470400-102477600	Weak transcription	Fetal Intestine Large	intestine
28	chr7:102470400-102477600	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:102470400-102477600	Weak transcription	Ovary	ovary
30	chr7:102470400-102479800	Weak transcription	Lung	lung
31	chr7:102470400-102480400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr7:102470400-102481600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:102470400-102482800	Weak transcription	Brain Anterior Caudate	brain
34	chr7:102470600-102477000	Weak transcription	Adipose Nuclei	Adipose
35	chr7:102470600-102481800	Weak transcription	Brain Angular Gyrus	brain
36	chr7:102470800-102475800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:102470800-102476800	Weak transcription	Hela-S3	cervix
38	chr7:102470800-102477000	Weak transcription	Aorta	Aorta
39	chr7:102470800-102484400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:102470800-102493200	Weak transcription	Primary T cells from cord blood	blood
41	chr7:102471200-102477000	Weak transcription	Fetal Stomach	stomach
42	chr7:102471600-102476800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:102471600-102480200	Weak transcription	Liver	Liver
44	chr7:102471800-102475800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:102471800-102500000	Weak transcription	Left Ventricle	heart
46	chr7:102472000-102476200	Weak transcription	Fetal Brain Male	brain
47	chr7:102472000-102484800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:102474600-102478000	Enhancers	HUVEC	blood vessel
49	chr7:102474800-102478000	Enhancers	HSMM	muscle
50	chr7:102475000-102476000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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