Variant report

Variant	rs1964242
Chromosome Location	chr7:99976703-99976704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99974887..99976892-chr7:99985893..99988252,2	K562	blood:
2	chr7:99966465..99969191-chr7:99975773..99977859,2	K562	blood:
3	chr7:99974792..99977177-chr7:100024957..100027235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1000215	0.84[ASN][1000 genomes]
rs10085549	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059129	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1063945	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761253	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761306	1.00[ASN][1000 genomes]
rs11761426	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763414	0.84[ASN][1000 genomes]
rs11765869	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766917	0.83[ASN][1000 genomes]
rs11768933	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768967	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769057	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769886	0.84[ASN][1000 genomes]
rs11771241	0.84[ASN][1000 genomes]
rs11771419	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771799	1.00[ASN][1000 genomes]
rs11771936	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636980	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.84[ASN][1000 genomes]
rs2108269	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401739	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28490152	0.84[ASN][1000 genomes]
rs28495773	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660238	0.84[ASN][1000 genomes]
rs28680963	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087502	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35111986	0.84[ASN][1000 genomes]
rs35986051	1.00[ASN][1000 genomes]
rs3900792	0.84[ASN][1000 genomes]
rs3991498	0.81[EUR][1000 genomes]
rs3991564	0.90[EUR][1000 genomes]
rs41280971	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735533	0.88[AMR][1000 genomes];0.96[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	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6946768	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948685	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953749	0.84[ASN][1000 genomes]
rs6955367	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.84[ASN][1000 genomes]
rs6965207	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.84[ASN][1000 genomes]
rs6975563	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975660	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979910	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705866	1.00[AMR][1000 genomes];0.96[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	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401450	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401451	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	0.84[ASN][1000 genomes]
rs7783550	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786844	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792525	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792959	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7795656	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795805	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799894	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799901	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799932	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803454	0.84[ASN][1000 genomes]

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:44)

SNP	Gene	Cis/trans	Tissue	Source
rs1964242	PILRA	cis	Muscle Skeletal	GTEx
rs1964242	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs1964242	STAG3L5P	cis	Artery Aorta	GTEx
rs1964242	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs1964242	PILRB	cis	Muscle Skeletal	GTEx
rs1964242	PILRB	cis	Esophagus Mucosa	GTEx
rs1964242	PILRB	cis	Thyroid	GTEx
rs1964242	PILRA	cis	Esophagus Mucosa	GTEx
rs1964242	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs1964242	PILRA	cis	Thyroid	GTEx
rs1964242	PVRIG2P	cis	Heart Left Ventricle	GTEx
rs1964242	PVRIG2P	cis	Esophagus Muscularis	GTEx
rs1964242	STAG3L5P	cis	Muscle Skeletal	GTEx
rs1964242	PILRA	cis	Stomach	GTEx
rs1964242	PILRA	cis	Nerve Tibial	GTEx
rs1964242	STAG3L5P	cis	Nerve Tibial	GTEx
rs1964242	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs1964242	PILRB	cis	Artery Tibial	GTEx
rs1964242	PILRB	cis	Adipose Subcutaneous	GTEx
rs1964242	STAG3L5P	cis	Artery Tibial	GTEx
rs1964242	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs1964242	PILRA	cis	Adipose Subcutaneous	GTEx
rs1964242	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs1964242	PILRA	cis	Esophagus Muscularis	GTEx
rs1964242	PVRIG2P	cis	lung	GTEx
rs1964242	STAG3L5P	cis	lung	GTEx
rs1964242	PILRB	cis	Artery Aorta	GTEx
rs1964242	PILRB	cis	Nerve Tibial	GTEx
rs1964242	PILRB	cis	Heart Left Ventricle	GTEx
rs1964242	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs1964242	PVRIG2P	cis	Thyroid	GTEx
rs1964242	PVRIG2P	cis	Artery Tibial	GTEx
rs1964242	PILRA	cis	Artery Tibial	GTEx
rs1964242	PILRA	cis	Artery Aorta	GTEx
rs1964242	PILRB	cis	Whole Blood	GTEx
rs1964242	PVRIG2P	cis	Nerve Tibial	GTEx
rs1964242	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs1964242	PILRA	cis	Heart Left Ventricle	GTEx
rs1964242	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs1964242	PILRB	cis	Esophagus Muscularis	GTEx
rs1964242	STAG3L5P	cis	Thyroid	GTEx
rs1964242	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs1964242	PILRB	cis	lung	GTEx
rs1964242	STAG3L5P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99934000-99977600	Weak transcription	Fetal Brain Male	brain
2	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
3	chr7:99960400-99984800	Weak transcription	Pancreas	Pancrea
4	chr7:99960600-99977600	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:99960600-99985200	Weak transcription	Aorta	Aorta
6	chr7:99961400-99977400	Weak transcription	Brain Substantia Nigra	brain
7	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:99964800-99977600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:99965200-99976800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:99965200-99979200	Weak transcription	Right Ventricle	heart
11	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:99969400-99982600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:99969800-99977000	Weak transcription	Brain Germinal Matrix	brain
14	chr7:99970200-99978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:99970400-99982400	Weak transcription	Hela-S3	cervix
16	chr7:99970600-99978800	Weak transcription	Primary T cells from cord blood	blood
17	chr7:99970800-99981600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:99971000-99977600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:99971000-99979600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:99971400-99976800	Weak transcription	Placenta	Placenta
21	chr7:99971400-99977400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:99971400-99978000	Weak transcription	Fetal Stomach	stomach
23	chr7:99971400-99981600	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:99972200-99977400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:99972200-99984600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr7:99972600-99976800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:99972600-99977400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:99972600-99996000	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:99972800-99978000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:99972800-99979800	Weak transcription	Adipose Nuclei	Adipose
31	chr7:99972800-99987400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:99972800-99994800	Weak transcription	Spleen	Spleen
33	chr7:99973000-99981600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:99973000-99999400	Weak transcription	Brain Anterior Caudate	brain
35	chr7:99973600-99987400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:99974000-99977400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:99974000-99980200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:99974000-99980200	Weak transcription	K562	blood
39	chr7:99976200-99977400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr7:99976200-99998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:99976400-99977000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr7:99976600-99977400	Weak transcription	Primary B cells from cord blood	blood
43	chr7:99976600-99977600	Active TSS	GM12878-XiMat	blood
44	chr7:99976600-99978400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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