Variant report

Variant	rs55969052
Chromosome Location	chr7:99650317-99650318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:99650037-99651266	A549	lung:	n/a	chr7:99650970-99650978 chr7:99651063-99651084 chr7:99651068-99651086

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99613224..99616757-chr7:99646903..99650456,6	K562	blood:
2	chr7:99612024..99615373-chr7:99646672..99650813,5	MCF-7	breast:
3	chr7:99587259..99592938-chr7:99645564..99652306,10	MCF-7	breast:
4	chr7:99649498..99652902-chr7:99676481..99680212,4	MCF-7	breast:
5	chr7:99649620..99652426-chr7:99723088..99724906,3	K562	blood:
6	chr7:99641810..99643993-chr7:99649500..99651035,2	MCF-7	breast:
7	chr7:99634823..99637646-chr7:99648903..99650452,2	K562	blood:
8	chr7:99650255..99652403-chr7:99656167..99658758,2	K562	blood:
9	chr7:99645952..99651427-chr7:99695296..99699701,5	K562	blood:
10	chr7:99648783..99651423-chr7:99660813..99663074,2	K562	blood:
11	chr7:99643907..99646572-chr7:99647724..99651166,3	K562	blood:
12	chr7:99648921..99651370-chr7:99655512..99657168,2	K562	blood:
13	chr7:99613216..99614721-chr7:99649494..99651653,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZSCAN21	TF binding region
ENSG00000166508	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000235713	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000221838	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11558475	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11558476	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532238	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4308665	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4421299	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727445	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054049	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60697181	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67091024	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67110214	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68038211	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72615158	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7780686	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7796006	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803317	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941289	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55969052	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs55969052	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs55969052	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs55969052	PILRB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648000-99654600	Weak transcription	Ovary	ovary
2	chr7:99648200-99654400	Weak transcription	Primary T cells from cord blood	blood
3	chr7:99648200-99654600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:99648200-99654600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:99648200-99654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:99648200-99654600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:99648200-99654600	Weak transcription	Aorta	Aorta
8	chr7:99648200-99654600	Weak transcription	Esophagus	oesophagus
9	chr7:99648200-99654600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:99648400-99650600	Weak transcription	Brain Anterior Caudate	brain
11	chr7:99648400-99650600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:99648400-99650800	Weak transcription	Brain Angular Gyrus	brain
13	chr7:99648400-99651000	Enhancers	Liver	Liver
14	chr7:99648400-99651200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:99648400-99653800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:99648400-99654000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:99648400-99654200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:99648400-99654400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:99648400-99654400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:99648400-99654400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:99648400-99654400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:99648400-99654400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:99648400-99654400	Weak transcription	Fetal Lung	lung
24	chr7:99648400-99654400	Weak transcription	A549	lung
25	chr7:99648400-99654400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:99648400-99654600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:99648400-99654600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:99648400-99654600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:99648400-99654600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:99648400-99654600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:99648400-99654600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:99648400-99654600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:99648400-99654600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:99648400-99654600	Weak transcription	Adipose Nuclei	Adipose
35	chr7:99648400-99654600	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:99648400-99654600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:99648400-99654600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:99648400-99654600	Weak transcription	Gastric	stomach
39	chr7:99648400-99654600	Weak transcription	Left Ventricle	heart
40	chr7:99648400-99654600	Weak transcription	Lung	lung
41	chr7:99648400-99654600	Weak transcription	Pancreas	Pancrea
42	chr7:99648400-99654600	Weak transcription	Right Ventricle	heart
43	chr7:99648400-99654600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:99648400-99654600	Weak transcription	Thymus	Thymus
45	chr7:99648400-99654600	Weak transcription	HUVEC	blood vessel
46	chr7:99648400-99654600	Weak transcription	NH-A	brain
47	chr7:99648400-99654600	Weak transcription	Osteobl	bone
48	chr7:99648400-99654800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:99648400-99654800	Weak transcription	Psoas Muscle	Psoas
50	chr7:99648400-99655000	Weak transcription	Primary B cells from cord blood	blood

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