Variant report

Variant	rs2078024
Chromosome Location	chr15:49621610-49621611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10519211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519221	0.81[EUR][1000 genomes]
rs10519229	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1055254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114003	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11630318	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11632038	0.81[EUR][1000 genomes]
rs11632575	0.83[EUR][1000 genomes]
rs11633282	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11634636	0.82[EUR][1000 genomes]
rs11635005	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11635308	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs11635354	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11638314	0.82[EUR][1000 genomes]
rs11638606	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1580996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1580997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962147	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962187	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16962189	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962202	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962205	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962236	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962257	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs16962259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962416	1.00[CHB][hapmap]
rs17396612	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17396747	0.82[EUR][1000 genomes]
rs17397211	0.82[EUR][1000 genomes]
rs17400706	0.94[MEX][hapmap]
rs17473568	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs17475228	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs17476940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17477722	0.81[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs17478618	0.94[MEX][hapmap]
rs1835227	0.91[ASN][1000 genomes]
rs1874614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2059935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2127243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2163097	0.91[ASN][1000 genomes]
rs2169931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2279192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2413958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2899437	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3088333	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs35692325	0.82[EUR][1000 genomes]
rs3784630	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4362337	1.00[JPT][hapmap]
rs4396481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774539	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57252806	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57560518	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57749497	0.82[EUR][1000 genomes]
rs59112977	0.84[EUR][1000 genomes]
rs59356430	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60594237	0.82[EUR][1000 genomes]
rs61259878	0.81[EUR][1000 genomes]
rs7162633	0.85[EUR][1000 genomes]
rs7167474	0.82[EUR][1000 genomes]
rs7167852	0.86[EUR][1000 genomes]
rs7168633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173759	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7181656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7183899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73392233	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73392262	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73394324	0.82[EUR][1000 genomes]
rs73394331	0.82[EUR][1000 genomes]
rs73394333	0.82[EUR][1000 genomes]
rs73394339	0.82[EUR][1000 genomes]
rs73394355	0.82[EUR][1000 genomes]
rs73394357	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394359	0.81[EUR][1000 genomes]
rs73396206	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396235	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73396238	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73398223	0.85[EUR][1000 genomes]
rs73398243	0.84[EUR][1000 genomes]
rs73398272	0.82[EUR][1000 genomes]
rs73398276	0.82[EUR][1000 genomes]
rs8025550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027094	0.84[EUR][1000 genomes]
rs8028746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8029506	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030457	0.84[EUR][1000 genomes]
rs8031680	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs8033311	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040436	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2078024	FGF7	cis	Muscle Skeletal	GTEx
rs2078024	SECISBP2L	cis	parietal	SCAN
rs2078024	LCMT2	cis	parietal	SCAN
rs2078024	TRPM7	cis	cerebellum	SCAN
rs2078024	C15orf33	cis	cerebellum	SCAN
rs2078024	MFAP1	cis	cerebellum	SCAN
rs2078024	TNFAIP8L3	cis	parietal	SCAN
rs2078024	DUOXA2	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
2	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
6	chr15:49597200-49622200	Weak transcription	NH-A	brain
7	chr15:49597200-49624800	Weak transcription	Fetal Kidney	kidney
8	chr15:49597400-49624200	Weak transcription	K562	blood
9	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:49606400-49622200	Weak transcription	HSMM	muscle
11	chr15:49607000-49622200	Weak transcription	NHDF-Ad	bronchial
12	chr15:49607200-49623800	Weak transcription	Psoas Muscle	Psoas
13	chr15:49607600-49624400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:49607800-49622200	Weak transcription	Brain Substantia Nigra	brain
15	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:49610400-49622400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:49612000-49624200	Weak transcription	Lung	lung
19	chr15:49612200-49623200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
21	chr15:49612200-49639000	Weak transcription	NHEK	skin
22	chr15:49612600-49622200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
24	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:49613000-49622600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:49613000-49622600	Weak transcription	Brain Anterior Caudate	brain
28	chr15:49613000-49624400	Weak transcription	GM12878-XiMat	blood
29	chr15:49613000-49627600	Weak transcription	HUVEC	blood vessel
30	chr15:49613000-49628200	Weak transcription	Ovary	ovary
31	chr15:49613000-49633200	Weak transcription	Gastric	stomach
32	chr15:49613200-49623200	Weak transcription	HMEC	breast
33	chr15:49613200-49625000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:49613200-49625000	Weak transcription	Hela-S3	cervix
35	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:49613600-49622200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:49613600-49625400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:49613600-49633800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:49613600-49637200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
41	chr15:49613800-49625000	Weak transcription	Fetal Brain Female	brain
42	chr15:49613800-49632600	Weak transcription	Fetal Thymus	thymus
43	chr15:49613800-49639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr15:49614000-49622000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:49614000-49622800	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:49614000-49624400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:49614000-49624400	Weak transcription	NHLF	lung
48	chr15:49614200-49622200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:49614200-49622200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:49614200-49622200	Weak transcription	Thymus	Thymus

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