Variant report

Variant	rs2857600
Chromosome Location	chr6:31582287-31582288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:31582163-31582472	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr6:31582012-31582737	HepG2	liver:	n/a	n/a
3	RCOR1	chr6:31582167-31582670	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:31582132-31582357	HepG2	liver:	n/a	n/a
5	TBP	chr6:31582179-31582617	GM12878	blood:	n/a	n/a
6	RUNX3	chr6:31581968-31582702	GM12878	blood:	n/a	n/a
7	EP300	chr6:31582111-31582476	GM12878	blood:	n/a	n/a
8	MXI1	chr6:31582164-31582433	GM12878	blood:	n/a	n/a
9	MYBL2	chr6:31581935-31582480	HepG2	liver:	n/a	n/a
10	IRF4	chr6:31582018-31582594	GM12878	blood:	n/a	n/a
11	BHLHE40	chr6:31582129-31582395	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:31582195-31582348	GM12878	blood:	n/a	n/a
13	REST	chr6:31582252-31582418	Hela-S3	cervix:	n/a	n/a
14	NFIC	chr6:31581984-31582380	HepG2	liver:	n/a	n/a
15	MAX	chr6:31582132-31582412	GM12878	blood:	n/a	n/a
16	HEY1	chr6:31581915-31582908	HepG2	liver:	n/a	n/a
17	IRF4	chr6:31581976-31582572	GM12878	blood:	n/a	n/a
18	ATF2	chr6:31582064-31582556	GM12878	blood:	n/a	n/a
19	NRF1	chr6:31582093-31582481	GM12878	blood:	n/a	n/a
20	MBD4	chr6:31581978-31582612	HepG2	liver:	n/a	n/a
21	MBD4	chr6:31582029-31582649	HepG2	liver:	n/a	n/a
22	YY1	chr6:31582071-31582397	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:31582254-31582334	A549	lung:	n/a	n/a
24	POLR2A	chr6:31582015-31582419	HepG2	liver:	n/a	n/a
25	SPI1	chr6:31582207-31582450	GM12878	blood:	n/a	chr6:31582361-31582370
26	SPI1	chr6:31582119-31582529	GM12891	blood:	n/a	chr6:31582361-31582370
27	MYBL2	chr6:31582023-31582981	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:31582037-31582342	HepG2	liver:	n/a	n/a
29	MXI1	chr6:31582086-31582419	HepG2	liver:	n/a	n/a
30	FOXA1	chr6:31582026-31582407	HepG2	liver:	n/a	n/a
31	SPI1	chr6:31582096-31582480	GM12878	blood:	n/a	chr6:31582361-31582370
32	SPI1	chr6:31581750-31583079	GM12878	blood:	n/a	chr6:31582944-31582957 chr6:31581971-31581984 chr6:31582946-31582955 chr6:31582361-31582370
33	RUNX3	chr6:31582078-31582512	GM12878	blood:	n/a	n/a
34	SPI1	chr6:31582100-31582548	GM12891	blood:	n/a	chr6:31582361-31582370
35	BHLHE40	chr6:31582156-31582471	GM12878	blood:	n/a	n/a
36	MTA3	chr6:31581920-31582696	GM12878	blood:	n/a	n/a
37	RCOR1	chr6:31582113-31582360	HepG2	liver:	n/a	n/a
38	WRNIP1	chr6:31582130-31582303	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:31582103-31582356	GM12878	blood:	n/a	n/a
40	GATA2	chr6:31582070-31582575	HUVEC	blood vessel:	n/a	chr6:31582433-31582447
41	STAT1	chr6:31582208-31582297	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31582285-31582335	Hela-S3	cervix:	n/a
2	chr6:31582285-31582335	AG10803	skin:	n/a
3	chr6:31582285-31582335	HRPEpiC	eye:	n/a
4	chr6:31582285-31582335	K562	blood:	n/a
5	chr6:31582285-31582335	ECC-1	luminal epithelium:	n/a
6	chr6:31582285-31582335	T-47D	breast:	n/a
7	chr6:31582285-31582335	GM12892	blood:	n/a
8	chr6:31582285-31582335	Hepatocyte	liver:	n/a
9	chr6:31582285-31582335	GM19239	blood:	n/a
10	chr6:31582285-31582335	PFSK-1	brain:	n/a
11	chr6:31582285-31582335	U87	brain:	n/a
12	chr6:31582285-31582335	NH-A	brain:	n/a
13	chr6:31582285-31582335	A549	lung:	n/a
14	chr6:31582285-31582335	HCM	heart:	n/a
15	chr6:31582285-31582335	HRCEpiC	kidney:	n/a
16	chr6:31582285-31582335	HPAEpiC	pulmonary alveolar:	n/a
17	chr6:31582285-31582335	NB4	blood:	n/a
18	chr6:31582285-31582335	AoSMC	blood vessel:	n/a
19	chr6:31582285-31582335	HNPCEpiC	eye:	n/a
20	chr6:31582285-31582335	HCF	heart:	n/a
21	chr6:31582285-31582335	SK-N-MC	brain:	n/a
22	chr6:31582285-31582335	HEK293	kidney:	embryo
23	chr6:31582285-31582335	HMEC	breast:	n/a
24	chr6:31582285-31582335	SKMC	muscle:	n/a
25	chr6:31582285-31582335	GM06990	blood:	n/a
26	chr6:31582285-31582335	PANC-1	pancreas:	n/a
27	chr6:31582285-31582335	NHDF-neo	bronchial:	n/a
28	chr6:31582285-31582335	HEEpiC	esophagus:	n/a
29	chr6:31582285-31582335	GM12891	blood:	n/a
30	chr6:31582285-31582335	GM12878	blood:	n/a
31	chr6:31582285-31582335	AG09309	skin:	n/a
32	chr6:31582285-31582335	Jurkat	blood:	n/a
33	chr6:31582285-31582335	HL-60	blood:	n/a
34	chr6:31582285-31582335	MCF10A-Er-Src	breast:	n/a
35	chr6:31582285-31582335	AG09319	gingival:	n/a
36	chr6:31582285-31582335	H1-hESC	embryonic stem cell:	embryo
37	chr6:31582285-31582335	NHBE	bronchial:	n/a
38	chr6:31582285-31582335	HCPEpiC	choroid plexus:	n/a
39	chr6:31582285-31582335	CMK	blood:	n/a
40	chr6:31582285-31582335	Caco-2	colon:	n/a
41	chr6:31582285-31582335	RPTEC	kidney:	n/a
42	chr6:31582285-31582335	HCT-116	colon:	n/a
43	chr6:31582285-31582335	IMR90	lung:	fetal
44	chr6:31582285-31582335	SAEC	small airway:	n/a
45	chr6:31582285-31582335	LNCaP	prostate:	n/a
46	chr6:31582285-31582335	PrEC	prostate:	n/a
47	chr6:31582285-31582335	MCF-7	breast:	n/a
48	chr6:31582285-31582335	HepG2	liver:	n/a
49	chr6:31582285-31582335	AG04449	skin:	fetal
50	chr6:31582285-31582335	ovcar-3	ovarian:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31539772..31542619-chr6:31581316..31584667,3	K562	blood:
2	chr6:31578073..31580095-chr6:31581694..31583880,2	MCF-7	breast:
3	chr6:31568999..31571023-chr6:31581321..31582957,2	MCF-7	breast:

No data

Variant related genes	Relation type
UQCRHP1	TF binding region
AIF1	TF binding region
AIF1	CpG island
UQCRHP1	CpG island
ENSG00000226979	Chromatin interaction
ENSG00000230622	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1043620	0.93[AMR][1000 genomes]
rs2736177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857594	0.89[EUR][1000 genomes]
rs2857609	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3115668	0.81[EUR][1000 genomes]
rs3115669	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117578	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130050	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130071	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130487	0.80[EUR][1000 genomes]
rs3130625	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3131376	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3131377	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9267551	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9267576	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS 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 miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2857600	HLA-C	cis	lymphoblastoid	GTEx
rs2857600	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs2857600	HLA-DRB5	cis	lymphoblastoid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31550000-31583200	Weak transcription	Right Atrium	heart
2	chr6:31581000-31582600	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:31581200-31582600	Enhancers	Fetal Thymus	thymus
4	chr6:31581200-31583000	Enhancers	Fetal Intestine Large	intestine
5	chr6:31581200-31583400	Enhancers	Fetal Intestine Small	intestine
6	chr6:31581400-31582600	Enhancers	Duodenum Mucosa	Duodenum
7	chr6:31581400-31583400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr6:31581400-31585200	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:31581600-31583400	Flanking Active TSS	HepG2	liver
10	chr6:31581800-31584400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:31582000-31582600	Enhancers	Liver	Liver
12	chr6:31582000-31582800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr6:31582000-31582800	Enhancers	K562	blood
14	chr6:31582000-31583000	Enhancers	Adipose Nuclei	Adipose
15	chr6:31582000-31583000	Enhancers	Placenta	Placenta
16	chr6:31582000-31583000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:31582000-31583000	Enhancers	Dnd41	blood
18	chr6:31582000-31583200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:31582000-31583200	Enhancers	Fetal Kidney	kidney
20	chr6:31582000-31583200	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:31582000-31584000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:31582000-31584200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:31582000-31584200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:31582000-31584800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr6:31582000-31585200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:31582200-31582400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:31582200-31583000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr6:31582200-31583000	Enhancers	Primary T cells from cord blood	blood
29	chr6:31582200-31583000	Weak transcription	Spleen	Spleen
30	chr6:31582200-31583200	Enhancers	Thymus	Thymus
31	chr6:31582200-31583600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr6:31582200-31583600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:31582200-31584200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:31582200-31584200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:31582200-31584400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:31582200-31584400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr6:31582200-31584400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:31582200-31585000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:31582200-31587800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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