Variant report

Variant	rs41385644
Chromosome Location	chr7:108105243-108105244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108102855..108105698-chr7:108109300..108111309,2	K562	blood:
2	chr7:108092926..108094617-chr7:108105069..108107356,2	K562	blood:
3	chr7:108094678..108098834-chr7:108103652..108107753,7	MCF-7	breast:
4	chr7:108092671..108095154-chr7:108102924..108105484,2	MCF-7	breast:
5	chr7:107819408..107821670-chr7:108103371..108105401,2	K562	blood:
6	chr7:108103332..108105675-chr7:108106936..108109038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10487859	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11973105	0.91[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11981670	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12705470	0.91[EUR][1000 genomes]
rs13227836	0.81[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs13228190	0.90[EUR][1000 genomes]
rs13229488	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13238841	0.81[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs13245101	0.91[EUR][1000 genomes]
rs13245242	0.91[EUR][1000 genomes]
rs13307045	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13312593	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17155828	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17338441	0.91[EUR][1000 genomes]
rs17338462	0.85[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs17423043	0.85[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs17423119	0.85[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs17424206	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs194587	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2214913	0.91[EUR][1000 genomes]
rs2214914	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2214915	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2300048	0.81[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2300052	0.85[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs3202837	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33987381	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34218460	0.91[EUR][1000 genomes]
rs34333829	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34583262	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34814097	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34887057	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35436957	0.90[EUR][1000 genomes]
rs35617326	0.91[EUR][1000 genomes]
rs35880371	0.91[EUR][1000 genomes]
rs40843	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40845	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs40850	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40854	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40872	0.90[EUR][1000 genomes]
rs40875	0.92[EUR][1000 genomes]
rs40878	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs40880	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40882	0.83[EUR][1000 genomes]
rs40885	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40886	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40895	0.91[EUR][1000 genomes]
rs40899	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40900	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40901	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40902	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40908	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40910	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4992578	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56145857	0.88[EUR][1000 genomes]
rs59458537	0.89[EUR][1000 genomes]
rs60398019	0.88[EUR][1000 genomes]
rs60426977	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6466233	0.90[EUR][1000 genomes]
rs6466238	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66461825	0.91[EUR][1000 genomes]
rs67027479	0.91[EUR][1000 genomes]
rs67694466	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6947492	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6949637	0.91[EUR][1000 genomes]
rs6955152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6959023	0.90[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6976309	0.91[EUR][1000 genomes]
rs6976649	0.90[EUR][1000 genomes]
rs6976659	0.91[EUR][1000 genomes]
rs6976752	0.91[EUR][1000 genomes]
rs6976776	0.91[EUR][1000 genomes]
rs6976804	0.91[EUR][1000 genomes]
rs6978552	0.90[EUR][1000 genomes]
rs71213282	0.91[EUR][1000 genomes]
rs71568528	0.83[EUR][1000 genomes]
rs7784170	0.90[EUR][1000 genomes]
rs7786947	0.91[EUR][1000 genomes]
rs7790875	0.81[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs7806869	0.89[EUR][1000 genomes]
rs7807737	0.91[EUR][1000 genomes]
rs7807941	0.91[EUR][1000 genomes]
rs7811808	0.93[EUR][1000 genomes]
rs9649307	0.91[EUR][1000 genomes]
rs9649308	0.93[EUR][1000 genomes]
rs9785056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv967438	chr7:108105134-108108283	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs41385644	PRKAR2B	cis	parietal	SCAN
rs41385644	THAP5	cis	Muscle Skeletal	GTEx
rs41385644	THAP5	cis	lymphoblastoid	seeQTL
rs41385644	THAP5	cis	Esophagus Muscularis	GTEx
rs41385644	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs41385644	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
2	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:108100400-108106600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr7:108100800-108108800	Weak transcription	HUVEC	blood vessel
5	chr7:108101000-108119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:108101400-108116800	Weak transcription	Osteobl	bone
7	chr7:108101800-108108400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:108102200-108106800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
10	chr7:108102400-108137000	Weak transcription	NH-A	brain
11	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:108102600-108116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:108102600-108118200	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:108102800-108107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:108102800-108111000	Weak transcription	HSMM	muscle
16	chr7:108102800-108111200	Weak transcription	Adipose Nuclei	Adipose
17	chr7:108102800-108126400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
19	chr7:108103000-108111200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:108103200-108105600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr7:108103200-108115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:108103400-108105800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr7:108103600-108105800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr7:108103800-108105600	Enhancers	Thymus	Thymus
25	chr7:108104200-108111200	Weak transcription	Left Ventricle	heart
26	chr7:108104400-108106000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr7:108104400-108106400	Enhancers	Primary T cells from cord blood	blood
28	chr7:108104400-108116400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:108104800-108117400	Weak transcription	Dnd41	blood
30	chr7:108105000-108106200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:108105000-108116000	Weak transcription	Primary T cells fromperipheralblood	blood

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