Variant report

Variant	rs941287
Chromosome Location	chr7:99807473-99807474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99806814-99807762	K562	blood:	n/a	n/a
2	GATA2	chr7:99807135-99807486	K562	blood:	n/a	n/a
3	MTA3	chr7:99806225-99807796	GM12878	blood:	n/a	n/a
4	RCOR1	chr7:99807074-99807493	K562	blood:	n/a	n/a
5	POLR2A	chr7:99807360-99807548	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:99807223-99807825	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr7:99807386-99808036	A549	lung:	n/a	n/a
8	TEAD4	chr7:99806705-99807686	K562	blood:	n/a	n/a
9	POLR2A	chr7:99807260-99808408	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr7:99807368-99807624	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr7:99807413-99807596	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr7:99807077-99807946	MCF-7	breast:	n/a	n/a
13	POLR2A	chr7:99807257-99807727	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99806315..99809110-chr7:99809565..99811179,2	MCF-7	breast:
2	chr7:99806182..99808834-chr7:99809702..99811286,2	MCF-7	breast:
3	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
4	chr7:99724514..99726891-chr7:99806728..99809263,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC2-2	chr7:99806586-99809617	NONHSAT122347
2	lnc-GPC2-2	chr7:99806591-99809617	NONHSAT122348

No data

Variant related genes	Relation type
STAG3	TF binding region
ENSG00000242798	Chromatin interaction
ENSG00000066923	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1043915	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs1052482	0.84[AFR][1000 genomes]
rs1061230	0.86[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10953295	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138417	0.86[CHB][hapmap]
rs11764176	0.86[CHB][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap]
rs12666425	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs12705073	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13230744	0.96[YRI][hapmap]
rs1617502	0.84[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1618851	0.84[AFR][1000 genomes]
rs1623264	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs1624099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636975	0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1637001	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs1727123	0.82[AFR][1000 genomes]
rs1727124	0.82[AFR][1000 genomes]
rs1727128	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727129	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727130	0.84[AFR][1000 genomes]
rs1727132	0.82[AFR][1000 genomes]
rs1727133	0.86[ASW][hapmap];0.86[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727134	0.86[CHB][hapmap]
rs1727138	0.86[ASW][hapmap];0.86[CHB][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727140	0.86[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727143	0.86[EUR][1000 genomes]
rs1727145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859787	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1918353	0.85[JPT][hapmap]
rs2005763	0.82[AFR][1000 genomes]
rs2246713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405442	0.82[CHB][hapmap]
rs2528900	0.86[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2906646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950518	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950520	0.86[CHB][hapmap]
rs3735241	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735242	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779045	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs4299940	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729580	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66809776	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6948729	0.86[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs705867	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7794170	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs7799441	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7811662	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs858502	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs858506	0.86[CHB][hapmap]
rs858510	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs858513	0.86[CHB][hapmap]
rs866500	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs941287	PILRB	cis	cerebellum	SCAN
rs941287	AZGP1	cis	parietal	SCAN
rs941287	AP4M1	cis	cerebellum	SCAN
rs941287	PILRA	cis	parietal	SCAN
rs941287	PILRB	cis	multi-tissue	Pritchard
rs941287	C17orf59	trans	cerebellum	SCAN
rs941287	AP4M1	cis	multi-tissue	Pritchard
rs941287	PVRIG	cis	lymphoblastoid	seeQTL
rs941287	AP4M1	cis	Thyroid	GTEx
rs941287	GATS	cis	multi-tissue	Pritchard
rs941287	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs941287	PILRB	cis	parietal	SCAN
rs941287	MBLAC1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:99796000-99808400	Weak transcription	Brain Anterior Caudate	brain
5	chr7:99796400-99808800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
7	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
8	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:99798200-99811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:99798600-99810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
13	chr7:99799600-99808800	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:99802600-99808400	Weak transcription	HSMMtube	muscle
17	chr7:99803000-99808400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:99803000-99810600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:99803000-99816800	Weak transcription	Brain Angular Gyrus	brain
20	chr7:99803200-99808600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:99803200-99813600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:99803800-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:99805200-99818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:99805600-99807800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:99805600-99812800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr7:99805800-99808800	Enhancers	Primary T cells from cord blood	blood
27	chr7:99806000-99810000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:99806000-99810000	Flanking Active TSS	GM12878-XiMat	blood
29	chr7:99806000-99812400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr7:99806200-99807600	Enhancers	Fetal Muscle Leg	muscle
31	chr7:99806200-99807800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr7:99806200-99808800	Enhancers	Fetal Thymus	thymus
33	chr7:99806200-99809000	Enhancers	Fetal Stomach	stomach
34	chr7:99806200-99809200	Enhancers	Primary B cells from peripheral blood	blood
35	chr7:99806200-99809800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr7:99806600-99807600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr7:99806800-99809000	Weak transcription	HepG2	liver
38	chr7:99806800-99819000	Weak transcription	Fetal Lung	lung
39	chr7:99807000-99807600	Enhancers	Fetal Intestine Small	intestine
40	chr7:99807000-99808400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:99807000-99808600	Enhancers	Thymus	Thymus
42	chr7:99807000-99808800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr7:99807000-99808800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr7:99807200-99807600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr7:99807200-99808200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:99807200-99808400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:99807200-99808400	Weak transcription	Small Intestine	intestine
48	chr7:99807200-99808800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr7:99807200-99808800	Weak transcription	Liver	Liver
50	chr7:99807200-99808800	Weak transcription	Rectal Mucosa Donor 31	rectum

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