Variant report

Variant	rs1727129
Chromosome Location	chr7:99811002-99811003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99810552-99811053	GM12892	blood:	n/a	n/a
2	POLR2A	chr7:99810882-99811051	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99810654-99811077	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:99810553-99812339	PANC-1	pancreas:	n/a	n/a
5	FOSL2	chr7:99810989-99812412	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99810546-99811055	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:99810825-99812775	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99806182..99808834-chr7:99809702..99811286,2	MCF-7	breast:
2	chr7:99745511..99748040-chr7:99809267..99811160,3	MCF-7	breast:
3	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
4	chr7:99806315..99809110-chr7:99809565..99811179,2	MCF-7	breast:
5	chr7:99760958..99763450-chr7:99810400..99812602,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC2-2	chr7:99810646-99811247	NONHSAT122348

No data

Variant related genes	Relation type
ENSG00000239521	TF binding region
PVRIG	TF binding region
ENSG00000188186	Chromatin interaction
ENSG00000066923	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10953295	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12705073	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1624099	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727128	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727143	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1727145	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859787	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246713	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906646	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950518	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735241	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735242	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4299940	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729580	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66809776	0.90[AMR][1000 genomes]
rs705867	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7799441	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs858502	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858510	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941287	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv981557	chr7:99808038-99811640	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1727129	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs1727129	AP4M1	cis	Thyroid	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
5	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:99798200-99811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
9	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:99803000-99816800	Weak transcription	Brain Angular Gyrus	brain
12	chr7:99803200-99813600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:99805200-99818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:99805600-99812800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr7:99806000-99812400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:99806800-99819000	Weak transcription	Fetal Lung	lung
17	chr7:99807200-99828400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:99807200-99847000	Weak transcription	Fetal Kidney	kidney
19	chr7:99807400-99815200	Weak transcription	Pancreas	Pancrea
20	chr7:99807600-99818400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:99807800-99812000	Weak transcription	K562	blood
22	chr7:99808000-99815200	Enhancers	Primary B cells from cord blood	blood
23	chr7:99808400-99813600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:99808800-99811200	Enhancers	Duodenum Mucosa	Duodenum
25	chr7:99808800-99811600	Enhancers	Liver	Liver
26	chr7:99809000-99811400	Enhancers	HepG2	liver
27	chr7:99809000-99813400	Weak transcription	Brain Anterior Caudate	brain
28	chr7:99809000-99817600	Weak transcription	Small Intestine	intestine
29	chr7:99809200-99813000	Enhancers	Primary T cells from cord blood	blood
30	chr7:99809200-99817600	Weak transcription	Colonic Mucosa	Colon
31	chr7:99809200-99834800	Weak transcription	HSMMtube	muscle
32	chr7:99809400-99815000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr7:99809400-99817600	Weak transcription	Spleen	Spleen
34	chr7:99809400-99818200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:99809600-99811200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr7:99809600-99812400	Enhancers	Fetal Intestine Small	intestine
37	chr7:99809600-99815000	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:99809600-99815000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:99809600-99815200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:99809600-99816800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:99809600-99817600	Weak transcription	Dnd41	blood
42	chr7:99809600-99818600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:99809800-99811400	Enhancers	Fetal Intestine Large	intestine
44	chr7:99809800-99813800	Enhancers	Thymus	Thymus
45	chr7:99809800-99814400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:99809800-99815000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:99809800-99815000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:99809800-99815000	Enhancers	Fetal Thymus	thymus
49	chr7:99810000-99812000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:99810000-99813000	Weak transcription	Fetal Muscle Leg	muscle

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