Variant report

Variant	rs6943160
Chromosome Location	chr7:99872071-99872072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99871916-99872347	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99746174..99748056-chr7:99869608..99872452,2	K562	blood:

Variant related genes	Relation type
ENSG00000239521	TF binding region
GATS	TF binding region
ENSG00000188186	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10246243	0.86[EUR][1000 genomes]
rs10269641	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11531577	0.83[EUR][1000 genomes]
rs11762932	0.82[EUR][1000 genomes]
rs11771660	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12056000	0.87[EUR][1000 genomes]
rs2056726	0.83[EUR][1000 genomes]
rs2272343	0.83[EUR][1000 genomes]
rs56089143	0.86[EUR][1000 genomes]
rs59248100	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6947033	0.84[EUR][1000 genomes]
rs6953580	0.86[EUR][1000 genomes]
rs73161745	0.80[ASN][1000 genomes]
rs73399514	0.86[EUR][1000 genomes]
rs7782305	0.84[EUR][1000 genomes]
rs7786505	0.86[EUR][1000 genomes]
rs7789890	0.84[EUR][1000 genomes]
rs7801070	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9692044	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
3	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	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
5	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv888774	chr7:99807265-99951315	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	esv16057	chr7:99809377-99937347	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv3379367	chr7:99811760-99938687	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv3379649	chr7:99812207-99939196	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	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
13	esv3358931	chr7:99816130-99943645	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
14	esv3405423	chr7:99816156-99943860	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	esv3508070	chr7:99816206-99943813	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	esv3508071	chr7:99816206-99943813	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6943160	PILRA	cis	Thyroid	GTEx
rs6943160	STAG3	cis	brain	BrainEAC
rs6943160	STAG3	Cis_1M	lymphoblastoid	RTeQTL
rs6943160	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs6943160	STAG3L5P	cis	lung	GTEx
rs6943160	PILRB	cis	Artery Tibial	GTEx
rs6943160	PILRB	cis	Esophagus Mucosa	GTEx
rs6943160	PILRA	cis	Muscle Skeletal	GTEx
rs6943160	PILRB	cis	lung	GTEx
rs6943160	PILRB	cis	Nerve Tibial	GTEx
rs6943160	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs6943160	STAG3L5P	cis	Thyroid	GTEx
rs6943160	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs6943160	STAG3L5P	cis	Nerve Tibial	GTEx
rs6943160	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs6943160	STAG3	cis	cerebellar cortex	BrainEAC
rs6943160	PVRIG2P	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99870200-99880600	Weak transcription	Fetal Lung	lung
2	chr7:99870200-99884200	Weak transcription	Aorta	Aorta
3	chr7:99870200-99916800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:99870200-99932800	Weak transcription	Ovary	ovary
5	chr7:99870400-99872800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:99870400-99873000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:99870400-99873400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:99870400-99873600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:99870400-99873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:99870400-99873600	Weak transcription	Fetal Intestine Small	intestine
11	chr7:99870400-99876800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:99870400-99885000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:99870400-99886200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:99870400-99901600	Weak transcription	Thymus	Thymus
15	chr7:99870400-99904600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:99870400-99917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:99870400-99917000	Weak transcription	Fetal Muscle Leg	muscle
18	chr7:99870400-99917600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:99870400-99923400	Weak transcription	Fetal Intestine Large	intestine
20	chr7:99870400-99932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:99870600-99873000	Weak transcription	Brain Angular Gyrus	brain
22	chr7:99870600-99873600	Weak transcription	Fetal Stomach	stomach
23	chr7:99870600-99874800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:99870600-99879800	Weak transcription	A549	lung
25	chr7:99870600-99880800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:99870600-99886400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:99870600-99887800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr7:99870600-99888400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:99870600-99888600	Weak transcription	GM12878-XiMat	blood
30	chr7:99870600-99890000	Weak transcription	Fetal Thymus	thymus
31	chr7:99870600-99898800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:99870600-99904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:99870600-99916800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:99870600-99923400	Weak transcription	Spleen	Spleen
35	chr7:99870600-99926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:99870600-99932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:99870800-99882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:99870800-99904600	Weak transcription	Dnd41	blood
39	chr7:99871000-99872200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:99871000-99886200	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:99871000-99917000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr7:99871000-99923000	Weak transcription	Brain Germinal Matrix	brain

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