Variant report

Variant	rs10085549
Chromosome Location	chr7:99983135-99983136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99980237..99981770-chr7:99982971..99984554,2	K562	blood:
2	chr7:99982614..99984718-chr7:100006163..100007904,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 59 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1000215	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10241492	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1059129	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1063945	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11559117	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap]
rs11760536	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11761253	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761306	1.00[ASN][1000 genomes]
rs11761426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761725	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11761784	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs11763414	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11763511	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11765869	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766752	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap]
rs11766917	0.83[ASN][1000 genomes]
rs11768933	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768967	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769057	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11769886	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11771241	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11771419	0.84[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771799	1.00[ASN][1000 genomes]
rs11771936	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773661	0.85[CEU][hapmap]
rs1636980	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.91[CEU][hapmap]
rs1964242	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.84[ASN][1000 genomes]
rs2108269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap]
rs2406255	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs28401739	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28490152	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs28495773	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578163	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs28660238	0.84[ASN][1000 genomes]
rs28680963	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087502	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs35111986	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs35986051	1.00[ASN][1000 genomes]
rs3900792	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3991498	0.83[EUR][1000 genomes]
rs3991564	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4074838	0.83[CHD][hapmap];1.00[GIH][hapmap]
rs41280971	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472444	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap]
rs61735533	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66632384	0.84[ASN][1000 genomes]
rs67163493	0.84[ASN][1000 genomes]
rs67315960	0.84[ASN][1000 genomes]
rs67471932	0.84[ASN][1000 genomes]
rs68116612	0.84[ASN][1000 genomes]
rs6945952	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6946768	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948685	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953749	0.84[ASN][1000 genomes]
rs6955362	0.85[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap]
rs6955367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.84[ASN][1000 genomes]
rs6965207	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965458	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.84[ASN][1000 genomes]
rs6975514	0.85[CEU][hapmap]
rs6975563	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6979910	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705866	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161745	0.85[ASN][1000 genomes]
rs73161759	0.84[ASN][1000 genomes]
rs73161762	0.84[ASN][1000 genomes]
rs73401443	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401450	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401451	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341507	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7783550	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]
rs7786844	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787620	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7792525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792959	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7794485	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7795656	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795805	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799894	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799901	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799932	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803454	0.84[ASN][1000 genomes]
rs7809801	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][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
rs10085549	STAG3L5P	cis	Stomach	GTEx
rs10085549	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs10085549	CNPY4	cis	cerebellum	SCAN
rs10085549	PILRB	cis	parietal	SCAN
rs10085549	GNB2	cis	parietal	SCAN
rs10085549	PVRIG2P	cis	Heart Left Ventricle	GTEx
rs10085549	PILRB	cis	cerebellum	SCAN
rs10085549	PILRB	cis	Thyroid	GTEx
rs10085549	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs10085549	PILRB	cis	Artery Aorta	GTEx
rs10085549	STAG3L5P	cis	Muscle Skeletal	GTEx
rs10085549	PILRA	cis	Thyroid	GTEx
rs10085549	PVRIG2P	cis	Thyroid	GTEx
rs10085549	ORAI2	cis	cerebellum	SCAN
rs10085549	STAG3L5P	cis	Nerve Tibial	GTEx
rs10085549	PILRA	cis	Esophagus Mucosa	GTEx
rs10085549	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs10085549	PVRIG2P	cis	lung	GTEx
rs10085549	PILRA	cis	Stomach	GTEx
rs10085549	STAG3L5P	cis	lung	GTEx
rs10085549	PILRB	cis	Nerve Tibial	GTEx
rs10085549	PVRIG	cis	lymphoblastoid	seeQTL
rs10085549	PILRB	cis	lymphoblastoid	seeQTL
rs10085549	PILRB	cis	Muscle Skeletal	GTEx
rs10085549	ZCWPW1	cis	parietal	SCAN
rs10085549	STAG3L5P	cis	Artery Aorta	GTEx
rs10085549	PILRB	cis	Esophagus Muscularis	GTEx
rs10085549	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs10085549	PVRIG2P	cis	Nerve Tibial	GTEx
rs10085549	PILRB	cis	Whole Blood	GTEx
rs10085549	STAG3	cis	lymphoblastoid	seeQTL
rs10085549	PILRB	cis	Artery Tibial	GTEx
rs10085549	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs10085549	PILRA	cis	Muscle Skeletal	GTEx
rs10085549	PILRB	cis	multi-tissue	Pritchard
rs10085549	PILRB	cis	Esophagus Mucosa	GTEx
rs10085549	PVRIG2P	cis	Artery Tibial	GTEx
rs10085549	STAG3L5P	cis	Thyroid	GTEx
rs10085549	PILRB	cis	Adipose Subcutaneous	GTEx
rs10085549	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs10085549	PILRA	cis	Esophagus Muscularis	GTEx
rs10085549	PILRA	cis	Heart Left Ventricle	GTEx
rs10085549	STAG3L5P	cis	Artery Tibial	GTEx
rs10085549	PILRA	cis	cerebellum	SCAN
rs10085549	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs10085549	PILRA	cis	Nerve Tibial	GTEx
rs10085549	PILRA	cis	Artery Tibial	GTEx
rs10085549	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs10085549	PILRB	cis	lung	GTEx
rs10085549	PILRA	cis	parietal	SCAN
rs10085549	GATS	cis	parietal	SCAN
rs10085549	PILRA	cis	Artery Aorta	GTEx
rs10085549	PILRA	cis	Adipose Subcutaneous	GTEx
rs10085549	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs10085549	ZCWPW1	cis	cerebellum	SCAN
rs10085549	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs10085549	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs10085549	PILRB	cis	Heart Left Ventricle	GTEx
rs10085549	PVRIG	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
2	chr7:99960400-99984800	Weak transcription	Pancreas	Pancrea
3	chr7:99960600-99985200	Weak transcription	Aorta	Aorta
4	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:99972200-99984600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:99972600-99996000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:99972800-99987400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:99972800-99994800	Weak transcription	Spleen	Spleen
10	chr7:99973000-99999400	Weak transcription	Brain Anterior Caudate	brain
11	chr7:99973600-99987400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:99976200-99998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:99977000-99989800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:99980600-99985600	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:99981200-99983200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:99981800-99987400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:99982600-99984200	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr7:99982600-99985000	Weak transcription	Adipose Nuclei	Adipose
19	chr7:99982800-99983200	Enhancers	GM12878-XiMat	blood
20	chr7:99982800-99984600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:99982800-99987400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:99983000-99983200	Enhancers	HSMMtube	muscle

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