Variant report

Variant	rs7783550
Chromosome Location	chr7:99987805-99987806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99983658..99989026-chr7:100025931..100030707,8	MCF-7	breast:
2	chr7:99974887..99976892-chr7:99985893..99988252,2	K562	blood:
3	chr7:99987127..99989737-chr7:99990266..99992845,2	K562	blood:
4	chr7:99983162..99986044-chr7:99986515..99990013,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 59 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1000215	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10085549	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1059129	0.85[ASN][1000 genomes]
rs1063945	1.00[ASN][1000 genomes]
rs1073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11559117	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11760536	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs11761253	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[ASN][1000 genomes]
rs11761306	1.00[ASN][1000 genomes]
rs11761426	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761725	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11761784	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11763414	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11763511	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11764818	0.85[EUR][1000 genomes]
rs11765869	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766752	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11766917	0.83[ASN][1000 genomes]
rs11768933	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768967	1.00[ASN][1000 genomes]
rs11769057	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11769886	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11771241	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11771419	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771799	1.00[ASN][1000 genomes]
rs11771936	1.00[ASN][1000 genomes]
rs11773661	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1636980	1.00[ASN][1000 genomes]
rs1962269	0.92[CEU][hapmap]
rs1964242	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2108269	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2406255	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs28401739	0.92[ASN][1000 genomes]
rs28490152	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28495773	1.00[ASN][1000 genomes]
rs28578163	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs28629346	0.81[EUR][1000 genomes]
rs28660238	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28680963	1.00[ASN][1000 genomes]
rs3087502	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs35111986	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35986051	1.00[ASN][1000 genomes]
rs3900792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074838	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs41280971	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472444	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4989959	0.85[EUR][1000 genomes]
rs60257855	0.85[EUR][1000 genomes]
rs61735533	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66632384	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67163493	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67196635	0.85[EUR][1000 genomes]
rs67239991	0.83[EUR][1000 genomes]
rs67315960	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67471932	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67483801	0.85[EUR][1000 genomes]
rs68116612	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6945952	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6946768	1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948685	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953749	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6955362	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6955367	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6962151	0.85[EUR][1000 genomes]
rs6965207	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965458	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6970828	0.82[EUR][1000 genomes]
rs6975514	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6975563	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975660	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6979910	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs705866	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161745	0.85[ASN][1000 genomes]
rs73161759	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73161762	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73401443	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401450	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401451	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403312	0.85[EUR][1000 genomes]
rs7341507	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7786844	1.00[ASN][1000 genomes]
rs7787620	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7792525	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792959	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7794485	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs7795656	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795805	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799894	1.00[ASN][1000 genomes]
rs7799901	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799932	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800667	0.84[EUR][1000 genomes]
rs7803454	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7809801	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][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	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases

mRNA abundance (count:59)

SNP	Gene	Cis/trans	Tissue	Source
rs7783550	PILRA	cis	Artery Aorta	GTEx
rs7783550	MEPCE	cis	lymphoblastoid	seeQTL
rs7783550	PILRB	cis	Heart Left Ventricle	GTEx
rs7783550	PILRB	cis	Adipose Subcutaneous	GTEx
rs7783550	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs7783550	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs7783550	PVRIG	cis	cerebellum	SCAN
rs7783550	GNB2	cis	parietal	SCAN
rs7783550	GATS	cis	multi-tissue	Pritchard
rs7783550	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs7783550	PILRB	cis	Whole Blood	GTEx
rs7783550	PILRA	cis	Muscle Skeletal	GTEx
rs7783550	PILRB	cis	multi-tissue	Pritchard
rs7783550	PILRA	cis	Adipose Subcutaneous	GTEx
rs7783550	STAG3L5P	cis	Artery Aorta	GTEx
rs7783550	PILRB	cis	Thyroid	GTEx
rs7783550	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs7783550	PILRB	cis	lymphoblastoid	seeQTL
rs7783550	PVRIG2P	cis	Nerve Tibial	GTEx
rs7783550	STAG3L5P	cis	Artery Tibial	GTEx
rs7783550	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs7783550	PVRIG2P	cis	Artery Tibial	GTEx
rs7783550	PMS2	trans	multi-tissue	Pritchard
rs7783550	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs7783550	CNPY4	cis	cerebellum	SCAN
rs7783550	PILRB	cis	parietal	SCAN
rs7783550	PILRB	cis	Esophagus Mucosa	GTEx
rs7783550	ZCWPW1	cis	cerebellum	SCAN
rs7783550	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs7783550	ZCWPW1	cis	parietal	SCAN
rs7783550	PILRB	cis	cerebellum	SCAN
rs7783550	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs7783550	PILRA	cis	Artery Tibial	GTEx
rs7783550	PILRB	cis	Nerve Tibial	GTEx
rs7783550	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs7783550	STAG3L5P	cis	lung	GTEx
rs7783550	STAG3L5P	cis	Stomach	GTEx
rs7783550	PILRB	cis	Artery Aorta	GTEx
rs7783550	PILRB	cis	Artery Tibial	GTEx
rs7783550	PILRA	cis	Thyroid	GTEx
rs7783550	PILRA	cis	Esophagus Muscularis	GTEx
rs7783550	PVRIG2P	cis	lung	GTEx
rs7783550	PILRB	cis	lung	GTEx
rs7783550	STAG3L5P	cis	Thyroid	GTEx
rs7783550	PILRA	cis	parietal	SCAN
rs7783550	STAG3L5P	cis	Nerve Tibial	GTEx
rs7783550	PILRB	cis	Muscle Skeletal	GTEx
rs7783550	GATS	cis	parietal	SCAN
rs7783550	PILRB	cis	Esophagus Muscularis	GTEx
rs7783550	PILRA	cis	cerebellum	SCAN
rs7783550	PILRA	cis	Heart Left Ventricle	GTEx
rs7783550	STAG3L5P	cis	Muscle Skeletal	GTEx
rs7783550	PILRA	cis	Nerve Tibial	GTEx
rs7783550	PILRA	cis	Stomach	GTEx
rs7783550	PMS2P1	cis	Thyroid	GTEx
rs7783550	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs7783550	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs7783550	PVRIG2P	cis	Thyroid	GTEx
rs7783550	PILRA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
2	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:99972600-99996000	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:99972800-99994800	Weak transcription	Spleen	Spleen
6	chr7:99973000-99999400	Weak transcription	Brain Anterior Caudate	brain
7	chr7:99976200-99998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:99977000-99989800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:99985000-99988800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:99985400-99988000	Weak transcription	Fetal Heart	heart
11	chr7:99985400-99989600	Weak transcription	GM12878-XiMat	blood
12	chr7:99985400-99994800	Weak transcription	Ovary	ovary
13	chr7:99985600-99989600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr7:99987200-99991000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:99987400-99988200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:99987400-99988600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:99987400-99988600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:99987400-99988600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:99987400-99988600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:99987400-99988600	Enhancers	Pancreas	Pancrea
21	chr7:99987600-99988000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:99987600-99988200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:99987600-99988600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr7:99987600-99988600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr7:99987800-99988000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr7:99987800-99988200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:99987800-99988600	Enhancers	Gastric	stomach
28	chr7:99987800-99989000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr7:99987800-99989600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:99987800-100025400	Weak transcription	Right Ventricle	heart

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