Variant report

Variant	rs2300048
Chromosome Location	chr7:108066989-108066990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108066488..108068801-chr7:108095390..108097145,2	MCF-7	breast:
2	chr7:108066256..108068604-chr7:108069393..108073824,4	K562	blood:
3	chr7:108013080..108015754-chr7:108065360..108068339,2	MCF-7	breast:
4	chr7:108066612..108068536-chr7:108068946..108071866,2	K562	blood:
5	chr7:108066199..108068396-chr7:108077458..108079892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10245718	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs10487859	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs11971972	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11973105	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11973823	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11974559	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11976021	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11979596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11981670	0.86[EUR][1000 genomes]
rs11983900	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12669879	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12705470	0.90[CEU][hapmap];0.82[GIH][hapmap];0.91[MKK][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13222628	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13227836	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228190	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13229488	0.86[EUR][1000 genomes]
rs13238841	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13245101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13245242	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13307045	0.85[EUR][1000 genomes]
rs13312593	0.85[EUR][1000 genomes]
rs17155637	0.80[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs17155828	0.86[EUR][1000 genomes]
rs17338441	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17338462	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17421351	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17423043	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17423119	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17424206	0.86[EUR][1000 genomes]
rs194587	0.86[EUR][1000 genomes]
rs2108252	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2108253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2214913	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2214914	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2214915	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2300040	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300052	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2395995	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3202837	0.86[EUR][1000 genomes]
rs33987381	0.90[EUR][1000 genomes]
rs34218460	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34333829	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34583262	0.90[EUR][1000 genomes]
rs34814097	0.86[EUR][1000 genomes]
rs34887057	0.86[EUR][1000 genomes]
rs35429156	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35436957	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35617326	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35880371	0.82[EUR][1000 genomes]
rs40843	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs40845	0.87[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs40850	0.86[EUR][1000 genomes]
rs40854	0.84[EUR][1000 genomes]
rs40872	0.83[EUR][1000 genomes]
rs40875	0.84[EUR][1000 genomes]
rs40878	0.84[EUR][1000 genomes]
rs40880	0.82[EUR][1000 genomes]
rs40885	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs40886	0.82[EUR][1000 genomes]
rs40895	0.83[EUR][1000 genomes]
rs40899	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs40900	0.83[EUR][1000 genomes]
rs40901	0.83[EUR][1000 genomes]
rs40902	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs40908	0.83[EUR][1000 genomes]
rs40910	0.81[EUR][1000 genomes]
rs41385644	0.81[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs4992578	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56145857	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59458537	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60398019	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60426977	0.84[EUR][1000 genomes]
rs6466224	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6466225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6466226	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6466233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6466238	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs66461825	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67027479	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67694466	0.84[EUR][1000 genomes]
rs6947492	0.86[EUR][1000 genomes]
rs6949637	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6954366	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6955152	0.86[EUR][1000 genomes]
rs6959023	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6959409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6960478	0.85[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6966107	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6967368	0.82[CEU][hapmap];0.89[GIH][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6969521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6976309	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6976649	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6976659	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6976752	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6976776	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6976804	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6978552	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71213282	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7784170	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7786947	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7790875	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792321	0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[ASN][1000 genomes]
rs7797885	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7806869	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7807737	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7807941	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7811808	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9649307	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9649308	0.89[EUR][1000 genomes]
rs9785056	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2300048	CDHR3	cis	cerebellum	SCAN
rs2300048	THAP5	cis	normal skin	skin_eQTL
rs2300048	THAP5	cis	Esophagus Muscularis	GTEx
rs2300048	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108056800-108071000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:108057200-108067200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:108057600-108067000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:108057600-108069000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:108058800-108067400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:108058800-108071200	Weak transcription	Pancreas	Pancrea
7	chr7:108059800-108073400	Weak transcription	Fetal Brain Female	brain
8	chr7:108061200-108067000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:108063200-108070400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:108064000-108068000	Weak transcription	HUVEC	blood vessel
11	chr7:108065000-108070000	Enhancers	A549	lung
12	chr7:108065000-108071000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:108065400-108067400	Enhancers	HMEC	breast
14	chr7:108065800-108067000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:108065800-108067200	Enhancers	NHEK	skin
16	chr7:108066000-108067200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:108066200-108067000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:108066400-108068200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:108066800-108067200	Enhancers	Brain Angular Gyrus	brain

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