Variant report

Variant	rs28495773
Chromosome Location	chr7:99943583-99943584
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99943384-99944385	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:99943561-99944470	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99943473-99944311	GM12892	blood:	n/a	n/a
4	CTCF	chr7:99943440-99943590	BJ	skin:	n/a	n/a
5	POLR2A	chr7:99943496-99943902	GM12891	blood:	n/a	n/a
6	CTCF	chr7:99943440-99943590	NHLF	lung:	n/a	n/a
7	CTCF	chr7:99943440-99943590	AoAF	blood vessel:	n/a	n/a
8	POLR2A	chr7:99943282-99944354	GM12878	blood:	n/a	n/a
9	CTCF	chr7:99943460-99943610	HEEpiC	esophagus:	n/a	n/a
10	POLR2A	chr7:99943554-99943889	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99942281..99944536-chr7:100038040..100040733,2	K562	blood:
2	chr7:99815070..99817106-chr7:99943505..99945105,2	MCF-7	breast:
3	chr7:99687225..99689222-chr7:99941208..99944059,2	K562	blood:
4	chr7:99851711..99854330-chr7:99942995..99944936,2	K562	blood:
5	chr7:99942706..99944799-chr7:99946310..99948401,2	MCF-7	breast:
6	chr7:99943342..99945530-chr7:99954534..99957362,2	K562	blood:
7	chr7:99942279..99946162-chr7:100025896..100028763,3	K562	blood:
8	chr7:99942126..99946670-chr7:99946770..99950661,7	K562	blood:
9	chr7:99941805..99944661-chr7:100026023..100029271,5	K562	blood:
10	chr7:99941834..99943595-chr7:99990991..99992805,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PILRB-1	chr7:99943488-99943591	NONHSAT122362

No data

Variant related genes	Relation type
PMS2P1	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000121716	Chromatin interaction
ENSG00000213413	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000272752	Chromatin interaction
ENSG00000168090	Chromatin interaction
ENSG00000235333	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 45 )

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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059129	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1063945	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761253	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761306	1.00[ASN][1000 genomes]
rs11761426	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763414	0.84[ASN][1000 genomes]
rs11765869	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766917	0.83[ASN][1000 genomes]
rs11768933	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768967	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769057	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769886	0.84[ASN][1000 genomes]
rs11771241	0.84[ASN][1000 genomes]
rs11771419	1.00[ASN][1000 genomes]
rs11771799	1.00[ASN][1000 genomes]
rs11771936	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636980	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964242	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.84[ASN][1000 genomes]
rs2108269	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401739	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28490152	0.84[ASN][1000 genomes]
rs28660238	0.84[ASN][1000 genomes]
rs28680963	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087502	0.88[AMR][1000 genomes];0.91[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	0.86[EUR][1000 genomes]
rs3991564	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41280971	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735533	0.88[AMR][1000 genomes];0.91[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];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6946768	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948685	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953749	0.84[ASN][1000 genomes]
rs6955367	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.84[ASN][1000 genomes]
rs6965207	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965458	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.84[ASN][1000 genomes]
rs6975563	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975660	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979910	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705866	0.91[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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401450	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401451	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341507	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	0.84[ASN][1000 genomes]
rs7783550	1.00[ASN][1000 genomes]
rs7786844	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792525	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792959	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7795656	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795805	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799894	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799901	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799932	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803454	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv1830570	chr7:99901968-99945827	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	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
12	nsv888775	chr7:99940307-99961194	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:45)

SNP	Gene	Cis/trans	Tissue	Source
rs28495773	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs28495773	PILRB	cis	Nerve Tibial	GTEx
rs28495773	PILRA	cis	Thyroid	GTEx
rs28495773	STAG3L5P	cis	Artery Aorta	GTEx
rs28495773	PVRIG2P	cis	Thyroid	GTEx
rs28495773	PVRIG2P	cis	Esophagus Muscularis	GTEx
rs28495773	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs28495773	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs28495773	PILRA	cis	Muscle Skeletal	GTEx
rs28495773	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs28495773	PVRIG2P	cis	Nerve Tibial	GTEx
rs28495773	STAG3L5P	cis	lung	GTEx
rs28495773	PILRA	cis	Adipose Subcutaneous	GTEx
rs28495773	PILRB	cis	Artery Tibial	GTEx
rs28495773	PILRA	cis	Esophagus Mucosa	GTEx
rs28495773	PILRA	cis	Artery Aorta	GTEx
rs28495773	STAG3L5P	cis	Stomach	GTEx
rs28495773	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs28495773	PILRB	cis	lung	GTEx
rs28495773	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs28495773	PILRB	cis	Heart Left Ventricle	GTEx
rs28495773	PILRA	cis	Nerve Tibial	GTEx
rs28495773	PILRA	cis	Artery Tibial	GTEx
rs28495773	STAG3L5P	cis	Thyroid	GTEx
rs28495773	STAG3L5P	cis	Nerve Tibial	GTEx
rs28495773	PVRIG2P	cis	lung	GTEx
rs28495773	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs28495773	PILRA	cis	Heart Left Ventricle	GTEx
rs28495773	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs28495773	PILRB	cis	Thyroid	GTEx
rs28495773	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs28495773	PVRIG2P	cis	Artery Tibial	GTEx
rs28495773	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs28495773	PILRB	cis	Muscle Skeletal	GTEx
rs28495773	STAG3L5P	cis	Artery Tibial	GTEx
rs28495773	PILRB	cis	Esophagus Muscularis	GTEx
rs28495773	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs28495773	PILRA	cis	Stomach	GTEx
rs28495773	PILRA	cis	Esophagus Muscularis	GTEx
rs28495773	PVRIG2P	cis	Heart Left Ventricle	GTEx
rs28495773	PILRB	cis	multi-tissue	Pritchard
rs28495773	PILRB	cis	Adipose Subcutaneous	GTEx
rs28495773	PILRB	cis	Whole Blood	GTEx
rs28495773	PILRB	cis	Esophagus Mucosa	GTEx
rs28495773	STAG3L5P	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99934000-99977600	Weak transcription	Fetal Brain Male	brain
2	chr7:99934200-99943600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99934200-99943600	Weak transcription	HSMMtube	muscle
4	chr7:99934200-99944000	Weak transcription	Fetal Kidney	kidney
5	chr7:99934200-99950800	Weak transcription	Small Intestine	intestine
6	chr7:99934400-99943800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:99934400-99944000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:99934400-99944200	Weak transcription	Colonic Mucosa	Colon
9	chr7:99934400-99944200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:99934400-99944200	Weak transcription	Ovary	ovary
11	chr7:99934400-99963400	Weak transcription	Psoas Muscle	Psoas
12	chr7:99934800-99944800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:99934800-99963800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:99935400-99944000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:99935400-99944200	Weak transcription	Brain Germinal Matrix	brain
16	chr7:99935400-99962200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:99935400-99962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:99937600-99967800	Strong transcription	Fetal Stomach	stomach
19	chr7:99938400-99944800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr7:99938600-99949000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:99938600-99967400	Strong transcription	Fetal Brain Female	brain
22	chr7:99938800-99962400	Strong transcription	Dnd41	blood
23	chr7:99939200-99944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:99939200-99949600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:99939800-99943600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:99940600-99943600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:99940800-99943600	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:99940800-99943600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:99940800-99943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:99940800-99943800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:99940800-99943800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:99940800-99943800	Weak transcription	Thymus	Thymus
33	chr7:99940800-99944000	Weak transcription	Aorta	Aorta
34	chr7:99940800-99944000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:99940800-99944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:99940800-99944200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
38	chr7:99941000-99944000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:99941400-99944000	Enhancers	Primary B cells from cord blood	blood
40	chr7:99941400-99944200	Weak transcription	Esophagus	oesophagus
41	chr7:99942000-99943600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr7:99942000-99944000	Weak transcription	Gastric	stomach
43	chr7:99942600-99943600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr7:99942600-99943600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr7:99942600-99943600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr7:99942600-99943600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr7:99942600-99943600	Weak transcription	Spleen	Spleen
48	chr7:99942600-99943800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:99942600-99943800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:99942600-99943800	Weak transcription	Brain Inferior Temporal Lobe	brain

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