Variant report

Variant	rs6873611
Chromosome Location	chr5:95195558-95195559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr5:95194401-95195612	Hela-S3	cervix:	n/a	n/a
2	GTF2F1	chr5:95194351-95195703	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr5:95194055-95195835	A549	lung:	n/a	n/a
4	MYC	chr5:95194425-95195581	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr5:95193720-95195741	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:95194418-95196405	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr5:95194310-95195644	Hela-S3	cervix:	n/a	n/a
8	SMARCC1	chr5:95193756-95196313	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:95194362-95195769	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:95193203-95198379	IMR90	lung:	n/a	n/a
11	SMC3	chr5:95194317-95195669	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr5:95194011-95195787	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr5:95194009-95198385	HUVEC	blood vessel:	n/a	n/a
14	CHD2	chr5:95194373-95195560	Hela-S3	cervix:	n/a	n/a
15	TCF7L2	chr5:95194339-95195637	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:95193934-95201037	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr5:95193766-95195581	SK-N-SH	brain:	n/a	n/a
18	JUN	chr5:95194460-95196248	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:95193696-95201073	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr5:95194497-95195778	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr5:95194323-95195726	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:95194409-95196282	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr5:95194282-95195615	Hela-S3	cervix:	n/a	n/a
24	MAZ	chr5:95192747-95195753	IMR90	lung:	n/a	chr5:95193307-95193316
25	BRCA1	chr5:95194394-95195597	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:95192803..95195845-chr5:95402156..95405628,4	K562	blood:
2	chr5:95194068..95196070-chr5:95401310..95403656,2	K562	blood:
3	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
4	chr1:27986423..27987105-chr5:95195175..95195706,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf27-2	chr5:95194508-95195835	NONHSAT102871
2	lnc-C5orf27-2	chr5:95194508-95195836	NR_026936

No data

Variant related genes	Relation type
ENSG00000250362	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1004654	0.82[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476660	0.87[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12515492	1.00[CHD][hapmap]
rs12659828	0.88[TSI][hapmap]
rs1465446	0.82[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17366761	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6873611	ERAP2	cis	cerebellum	SCAN
rs6873611	SPATA9	cis	cerebellum	SCAN
rs6873611	CHD1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95188400-95195600	Enhancers	Fetal Heart	heart
3	chr5:95191800-95195800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:95191800-95195800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:95192000-95201400	Enhancers	Placenta	Placenta
6	chr5:95192200-95195800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:95192200-95199400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:95192400-95199200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr5:95193000-95196400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:95193400-95196000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:95193600-95196800	Weak transcription	Right Ventricle	heart
12	chr5:95193800-95196400	Flanking Active TSS	Hela-S3	cervix
13	chr5:95193800-95197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:95194000-95195600	Flanking Active TSS	HepG2	liver
15	chr5:95194000-95200800	Weak transcription	Gastric	stomach
16	chr5:95194200-95195600	Flanking Active TSS	A549	lung
17	chr5:95194200-95195800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:95194200-95199000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr5:95194600-95195600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:95194600-95196200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:95194600-95196600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:95194600-95197000	Weak transcription	Left Ventricle	heart
24	chr5:95194800-95195600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr5:95194800-95195800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr5:95194800-95196200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:95194800-95196800	Weak transcription	Fetal Intestine Large	intestine
28	chr5:95194800-95196800	Weak transcription	Fetal Intestine Small	intestine
29	chr5:95194800-95196800	Weak transcription	Fetal Kidney	kidney
30	chr5:95194800-95197000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:95194800-95197200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:95194800-95199400	Enhancers	Liver	Liver
33	chr5:95195000-95195600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr5:95195000-95195600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr5:95195000-95195600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:95195000-95195600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:95195000-95195600	Enhancers	Brain Anterior Caudate	brain
38	chr5:95195000-95195800	Enhancers	Brain Substantia Nigra	brain
39	chr5:95195000-95196000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:95195000-95196000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr5:95195000-95196000	Weak transcription	Primary B cells from cord blood	blood
42	chr5:95195000-95196000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:95195000-95196400	Enhancers	Brain Hippocampus Middle	brain
44	chr5:95195000-95196400	Enhancers	Pancreas	Pancrea
45	chr5:95195000-95196400	Enhancers	Dnd41	blood
46	chr5:95195000-95196600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr5:95195000-95196600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:95195000-95196600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:95195000-95196800	Weak transcription	Primary T cells from cord blood	blood
50	chr5:95195000-95196800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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