Variant report

Variant	rs1923187
Chromosome Location	chr6:24721667-24721668
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:551)
CpG islands
(count:61)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:551 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr6:24721067-24721892	HepG2	liver:	n/a	n/a
2	EBF1	chr6:24720953-24722332	GM12878	blood:	n/a	n/a
3	REST	chr6:24721531-24722074	PFSK-1	brain:	n/a	n/a
4	TAF1	chr6:24721279-24722164	HepG2	liver:	n/a	n/a
5	KAP1	chr6:24721093-24722265	HEK293	kidney:	n/a	n/a
6	SRF	chr6:24720840-24721806	ECC-1	luminal epithelium:	n/a	n/a
7	RCOR1	chr6:24720378-24722426	GM12878	blood:	n/a	n/a
8	EGR1	chr6:24721481-24721694	GM12878	blood:	n/a	chr6:24721634-24721647 chr6:24721635-24721649
9	FOXP2	chr6:24721336-24721719	SK-N-MC	brain:	n/a	n/a
10	NFATC1	chr6:24720298-24722239	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:24720466-24722160	HEK293	kidney:	n/a	n/a
12	POLR2A	chr6:24719540-24722490	NB4	blood:	n/a	n/a
13	POLR2A	chr6:24721500-24722147	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr6:24719873-24722157	Hela-S3	cervix:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
15	USF2	chr6:24721656-24722012	HepG2	liver:	n/a	n/a
16	RFX5	chr6:24720757-24722225	Hela-S3	cervix:	n/a	chr6:24722201-24722210
17	ZNF384	chr6:24720930-24722053	GM12878	blood:	n/a	n/a
18	IRF4	chr6:24721252-24722221	GM12878	blood:	n/a	n/a
19	CHD2	chr6:24720320-24722058	H1-hESC	embryonic stem cell:	n/a	chr6:24721471-24721481
20	TAF1	chr6:24720417-24722118	ECC-1	luminal epithelium:	n/a	n/a
21	STAT2	chr6:24720844-24722177	K562	blood:	n/a	chr6:24721669-24721680 chr6:24721667-24721682 chr6:24721441-24721448
22	TCF7L2	chr6:24720972-24722127	HCT-116	colon:	n/a	chr6:24721297-24721304
23	MXI1	chr6:24720822-24722108	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPD	chr6:24720292-24722191	K562	blood:	n/a	n/a
25	TCF12	chr6:24720535-24722285	A549	lung:	n/a	chr6:24721784-24721791
26	BHLHE40	chr6:24721022-24722089	A549	lung:	n/a	chr6:24721097-24721113
27	CTCF	chr6:24721147-24721936	GM12878	blood:	n/a	chr6:24721158-24721171
28	SMC3	chr6:24720379-24722082	Hela-S3	cervix:	n/a	chr6:24720650-24720660
29	POLR2A	chr6:24720256-24722275	Hela-S3	cervix:	n/a	n/a
30	BHLHE40	chr6:24720460-24722377	K562	blood:	n/a	chr6:24720625-24720641 chr6:24720633-24720649 chr6:24721097-24721113
31	EGR1	chr6:24720878-24721964	K562	blood:	n/a	chr6:24721634-24721647 chr6:24721635-24721649 chr6:24720993-24721003
32	YY1	chr6:24720401-24722056	ECC-1	luminal epithelium:	n/a	chr6:24721092-24721102 chr6:24720994-24721003 chr6:24720789-24720798
33	MYC	chr6:24720900-24722121	Hela-S3	cervix:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
34	POLR2A	chr6:24717288-24722666	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:24720241-24722389	SK-N-SH	brain:	n/a	n/a
36	YY1	chr6:24720373-24722142	HepG2	liver:	n/a	chr6:24722106-24722122 chr6:24721092-24721102 chr6:24720994-24721003 chr6:24720789-24720798
37	STAT5A	chr6:24721583-24722169	GM12878	blood:	n/a	chr6:24721669-24721680
38	MYC	chr6:24721342-24722131	HepG2	liver:	n/a	chr6:24721856-24721863 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
39	CEBPB	chr6:24721176-24722039	A549	lung:	n/a	n/a
40	USF2	chr6:24720555-24722212	GM12878	blood:	n/a	chr6:24720625-24720641 chr6:24720633-24720649 chr6:24721097-24721113
41	TBP	chr6:24720403-24722236	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr6:24720348-24722095	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr6:24719329-24722375	ProgFib	skin:	n/a	n/a
44	JUN	chr6:24720841-24722394	K562	blood:	n/a	chr6:24721563-24721574 chr6:24720993-24721002 chr6:24720994-24721003
45	SRF	chr6:24720745-24722103	MCF-7	breast:	n/a	n/a
46	CREB1	chr6:24720927-24721670	A549	lung:	n/a	n/a
47	SPI1	chr6:24721324-24721759	GM12891	blood:	n/a	n/a
48	SIX5	chr6:24720839-24722302	A549	lung:	n/a	n/a
49	POLR2A	chr6:24719230-24722689	GM19193	blood:	n/a	n/a
50	ELF1	chr6:24720854-24721900	K562	blood:	n/a	chr6:24721241-24721252

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:24721656-24721706	NH-A	brain:	n/a
2	chr6:24721656-24721706	ECC-1	luminal epithelium:	n/a
3	chr6:24721656-24721706	NT2-D1	testis:	n/a
4	chr6:24721656-24721706	HEK293	kidney:	embryo
5	chr6:24721656-24721706	NB4	blood:	n/a
6	chr6:24721656-24721706	HCM	heart:	n/a
7	chr6:24721656-24721706	AG09309	skin:	n/a
8	chr6:24721656-24721706	ovcar-3	ovarian:	n/a
9	chr6:24721656-24721706	HRCEpiC	kidney:	n/a
10	chr6:24721656-24721706	GM06990	blood:	n/a
11	chr6:24721656-24721706	NHBE	bronchial:	n/a
12	chr6:24721656-24721706	GM12892	blood:	n/a
13	chr6:24721656-24721706	HPAEpiC	pulmonary alveolar:	n/a
14	chr6:24721656-24721706	SK-N-MC	brain:	n/a
15	chr6:24721656-24721706	HCPEpiC	choroid plexus:	n/a
16	chr6:24721656-24721706	HIPEpiC	eye:	n/a
17	chr6:24721656-24721706	PFSK-1	brain:	n/a
18	chr6:24721656-24721706	HepG2	liver:	n/a
19	chr6:24721656-24721706	HEEpiC	esophagus:	n/a
20	chr6:24721656-24721706	Jurkat	blood:	n/a
21	chr6:24721656-24721706	ProgFib	skin:	n/a
22	chr6:24721656-24721706	HRE	kidney:	n/a
23	chr6:24721656-24721706	RPTEC	kidney:	n/a
24	chr6:24721656-24721706	AG09319	gingival:	n/a
25	chr6:24721656-24721706	Hepatocyte	liver:	n/a
26	chr6:24721656-24721706	AG04449	skin:	fetal
27	chr6:24721656-24721706	GM12891	blood:	n/a
28	chr6:24721656-24721706	HCT-116	colon:	n/a
29	chr6:24721656-24721706	HMEC	breast:	n/a
30	chr6:24721656-24721706	GM19239	blood:	n/a
31	chr6:24721656-24721706	T-47D	breast:	n/a
32	chr6:24721656-24721706	U87	brain:	n/a
33	chr6:24721656-24721706	PrEC	prostate:	n/a
34	chr6:24721656-24721706	K562	blood:	n/a
35	chr6:24721656-24721706	BJ	skin:	n/a
36	chr6:24721656-24721706	SKMC	muscle:	n/a
37	chr6:24721656-24721706	SK-N-SH	brain:	n/a
38	chr6:24721656-24721706	AG10803	skin:	n/a
39	chr6:24721656-24721706	NHDF-neo	bronchial:	n/a
40	chr6:24721656-24721706	AG04450	lung:	fetal
41	chr6:24721656-24721706	PANC-1	pancreas:	n/a
42	chr6:24721656-24721706	BE2_C	brain:	n/a
43	chr6:24721656-24721706	HL-60	blood:	n/a
44	chr6:24721656-24721706	LNCaP	prostate:	n/a
45	chr6:24721656-24721706	SAEC	small airway:	n/a
46	chr6:24721656-24721706	AoSMC	blood vessel:	n/a
47	chr6:24721656-24721706	SK-N-SH_RA	brain:	n/a
48	chr6:24721656-24721706	HRPEpiC	eye:	n/a
49	chr6:24721656-24721706	HCF	heart:	n/a
50	chr6:24721656-24721706	HUVEC	blood vessel:	n/a

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
2	chr6:24721486..24723774-chr6:24748539..24750202,2	K562	blood:
3	chr6:24719506..24722494-chr6:24741132..24743826,4	K562	blood:
4	chr6:24719119..24721965-chr6:26020764..26023234,2	MCF-7	breast:
5	chr6:24657655..24659922-chr6:24720349..24722391,2	K562	blood:
6	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
7	chr6:24719711..24722073-chr6:24797818..24801450,3	K562	blood:
8	chr6:24716219..24722234-chr6:24748111..24753033,8	K562	blood:
9	chr17:80186268..80187089-chr6:24721445..24722067,2	HCT-116	colon:
10	chr6:24718870..24722603-chr6:26025035..26028594,6	K562	blood:
11	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
12	chr5:36241334..36243447-chr6:24720553..24722359,2	K562	blood:
13	chr19:55727413..55728309-chr6:24721650..24722152,2	Hela-S3	cervix:
14	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
15	chr6:24718549..24722818-chr6:24771512..24777723,8	MCF-7	breast:
16	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
17	chr6:24720585..24722124-chr7:7679223..7680620,4	Hela-S3	cervix:
18	chr6:24719968..24721731-chr6:26234799..26237042,2	K562	blood:
19	chr6:24717870..24723661-chr6:24773711..24778808,16	MCF-7	breast:
20	chr1:36690058..36690572-chr6:24721190..24722056,2	Hela-S3	cervix:
21	chr18:32821000..32821510-chr6:24721408..24722055,2	Hela-S3	cervix:
22	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
23	chr6:24720760..24722445-chr6:24809512..24811592,2	K562	blood:
24	chr6:24665745..24668755-chr6:24718443..24722281,4	MCF-7	breast:
25	chr3:156806315..156807103-chr6:24721263..24721889,2	Hela-S3	cervix:
26	chr14:53416668..53418435-chr6:24720286..24722655,2	MCF-7	breast:
27	chr6:20401095..20405762-chr6:24718847..24722714,7	K562	blood:
28	chr6:20400126..20404982-chr6:24718144..24722714,11	K562	blood:
29	chr19:37018973..37019502-chr6:24721343..24721894,2	Hela-S3	cervix:
30	chr6:24719452..24722494-chr6:24742032..24745228,7	K562	blood:
31	chr6:24492199..24495699-chr6:24718792..24721987,5	K562	blood:

No data

Variant related genes	Relation type
C6orf62	TF binding region
C6orf62	CpG island
ENSG00000186812	Chromatin interaction
ENSG00000218806	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000073712	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000141526	Chromatin interaction
ENSG00000111913	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000272402	Chromatin interaction
ENSG00000272345	Chromatin interaction
ENSG00000260286	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000152620	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000224164	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11753290	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs16889633	1.00[CHD][hapmap]
rs2744549	1.00[CHD][hapmap]
rs2744550	1.00[CHD][hapmap]
rs2744559	1.00[CHD][hapmap]
rs2817191	1.00[CHD][hapmap]
rs2817195	1.00[CHD][hapmap]
rs3181228	0.87[CEU][hapmap]
rs4472344	1.00[CHD][hapmap]
rs4544900	0.87[CEU][hapmap]
rs6456632	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744621	1.00[CHD][hapmap]
rs7744939	1.00[CHD][hapmap]
rs7749794	1.00[CHD][hapmap]
rs7764860	1.00[CHD][hapmap]
rs7765904	0.87[CEU][hapmap]
rs7770041	1.00[CHD][hapmap]
rs9356943	0.93[CEU][hapmap]
rs9379685	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	esv3423914	chr6:24719198-24721746	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	63 gene(s)	inside rSNPs	diseases
6	esv3427775	chr6:24721388-24721895	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1923187	ENSG00000112308	cis	multi-tissue	Pritchard
rs1923187	C6orf62	Cis_1M	lymphoblastoid	RTeQTL
rs1923187	ZNF187	cis	cerebellum	SCAN
rs1923187	C6orf62	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24716400-24722400	Active TSS	Ovary	ovary
2	chr6:24716600-24722000	Active TSS	Stomach Mucosa	stomach
3	chr6:24716600-24722400	Active TSS	Right Ventricle	heart
4	chr6:24716800-24722400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:24716800-24722600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:24717000-24721800	Active TSS	NH-A	brain
7	chr6:24717000-24722200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:24717000-24722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:24717000-24722400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:24717000-24722400	Active TSS	Brain Angular Gyrus	brain
11	chr6:24717000-24722600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:24717400-24722200	Active TSS	Fetal Intestine Large	intestine
13	chr6:24717600-24722000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:24717600-24722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:24717600-24722200	Active TSS	HSMMtube	muscle
16	chr6:24717800-24722000	Active TSS	Fetal Intestine Small	intestine
17	chr6:24717800-24722000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:24717800-24722000	Active TSS	NHLF	lung
19	chr6:24717800-24722200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:24717800-24722400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr6:24717800-24722400	Active TSS	Psoas Muscle	Psoas
22	chr6:24717800-24722400	Active TSS	Thymus	Thymus
23	chr6:24718000-24722000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr6:24718000-24722200	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:24718000-24722400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr6:24718000-24722400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:24718000-24722600	Active TSS	Stomach Smooth Muscle	stomach
28	chr6:24718200-24722000	Active TSS	Placenta	Placenta
29	chr6:24718200-24722200	Active TSS	A549	lung
30	chr6:24718200-24722400	Active TSS	Brain Anterior Caudate	brain
31	chr6:24718400-24721800	Active TSS	Hela-S3	cervix
32	chr6:24718400-24722000	Active TSS	Small Intestine	intestine
33	chr6:24718400-24722200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:24718400-24722200	Active TSS	Left Ventricle	heart
35	chr6:24718400-24722200	Active TSS	Lung	lung
36	chr6:24718400-24722200	Active TSS	Placenta Amnion	Placenta Amnion
37	chr6:24718400-24722400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:24718600-24722000	Active TSS	Fetal Muscle Trunk	muscle
39	chr6:24718600-24722000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr6:24718600-24722000	Active TSS	HSMM	muscle
41	chr6:24718600-24722200	Active TSS	Brain Substantia Nigra	brain
42	chr6:24718800-24722000	Active TSS	Pancreas	Pancrea
43	chr6:24718800-24722200	Active TSS	Colonic Mucosa	Colon
44	chr6:24718800-24722600	Active TSS	NHDF-Ad	bronchial
45	chr6:24719000-24722000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:24719000-24722000	Active TSS	Duodenum Mucosa	Duodenum
47	chr6:24719000-24722400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:24719200-24722000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr6:24719200-24722000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:24719200-24722000	Active TSS	Colon Smooth Muscle	Colon

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