Variant report

Variant	rs7846259
Chromosome Location	chr8:54756213-54756214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr8:54755198-54756234	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:54755114-54756286	MCF-7	breast:	n/a	n/a
3	GABPA	chr8:54755553-54756314	SK-N-SH	brain:	n/a	n/a
4	REST	chr8:54755335-54756286	HL-60	blood:	n/a	n/a
5	REST	chr8:54755582-54756222	PFSK-1	brain:	n/a	n/a
6	SIN3AK20	chr8:54755325-54756219	PANC-1	pancreas:	n/a	n/a
7	GATA3	chr8:54756172-54756572	T-47D	breast:	n/a	n/a
8	POLR2A	chr8:54755454-54756256	ProgFib	skin:	n/a	n/a
9	POLR2A	chr8:54754999-54756642	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:54755375-54756521	GM12878	blood:	n/a	n/a
11	MYC	chr8:54755159-54756351	NB4	blood:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
12	MXI1	chr8:54755369-54756309	GM12878	blood:	n/a	chr8:54755843-54755852 chr8:54756015-54756024
13	BHLHE40	chr8:54755675-54756277	A549	lung:	n/a	chr8:54755915-54755931 chr8:54755842-54755855 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755866 chr8:54755859-54755868 chr8:54755844-54755853 chr8:54755852-54755873 chr8:54755843-54755852 chr8:54755858-54755867
14	POLR2A	chr8:54755044-54756690	Hela-S3	cervix:	n/a	n/a
15	MXI1	chr8:54754928-54756631	IMR90	lung:	n/a	chr8:54755843-54755852 chr8:54756015-54756024
16	POLR2A	chr8:54755304-54756256	MCF-7	breast:	n/a	n/a
17	POLR2A	chr8:54755368-54756452	IMR90	lung:	n/a	n/a
18	MAX	chr8:54755217-54756350	HCT-116	colon:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
19	POLR2A	chr8:54754832-54756276	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr8:54755120-54756632	K562	blood:	n/a	n/a
21	MAX	chr8:54755357-54756247	SK-N-SH	brain:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
22	ELF1	chr8:54755422-54756294	MCF-7	breast:	n/a	chr8:54755922-54755934
23	ZMIZ1	chr8:54755101-54756262	K562	blood:	n/a	n/a
24	ETS1	chr8:54755656-54756223	GM12878	blood:	n/a	chr8:54756107-54756117 chr8:54756057-54756068
25	RCOR1	chr8:54755486-54756214	GM12878	blood:	n/a	n/a
26	EP300	chr8:54755416-54756274	ECC-1	luminal epithelium:	n/a	chr8:54756057-54756066 chr8:54756101-54756117
27	CBX3	chr8:54755545-54756249	K562	blood:	n/a	chr8:54756155-54756166
28	ELF1	chr8:54755343-54756325	MCF-7	breast:	n/a	chr8:54755922-54755934
29	MAX	chr8:54755240-54756274	ECC-1	luminal epithelium:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
30	TCF12	chr8:54755126-54756323	A549	lung:	n/a	chr8:54756014-54756024
31	E2F6	chr8:54755485-54756274	A549	lung:	n/a	n/a
32	E2F6	chr8:54755292-54756335	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr8:54755079-54757792	GM12891	blood:	n/a	n/a
34	MAX	chr8:54755077-54756247	HepG2	liver:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
35	MYC	chr8:54755001-54756270	K562	blood:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
36	E2F4	chr8:54755903-54756282	GM12878	blood:	n/a	n/a
37	POLR2A	chr8:54755363-54756465	GM12878	blood:	n/a	n/a
38	PML	chr8:54755204-54756451	GM12878	blood:	n/a	chr8:54755259-54755267
39	JUND	chr8:54755124-54756378	H1-hESC	embryonic stem cell:	n/a	n/a
40	USF1	chr8:54755027-54756280	SK-N-SH	brain:	n/a	chr8:54755915-54755931 chr8:54755842-54755855 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755866 chr8:54755859-54755868 chr8:54755844-54755853 chr8:54755852-54755873 chr8:54755843-54755852 chr8:54755858-54755867
41	ELF1	chr8:54755331-54756300	GM12878	blood:	n/a	chr8:54755922-54755934
42	ELK4	chr8:54755631-54756344	Hela-S3	cervix:	n/a	n/a
43	E2F6	chr8:54755658-54756307	H1-hESC	embryonic stem cell:	n/a	n/a
44	MTA3	chr8:54755169-54756358	GM12878	blood:	n/a	n/a
45	NFIC	chr8:54755525-54756232	GM12878	blood:	n/a	chr8:54755995-54756023
46	RFX5	chr8:54755052-54756306	Hela-S3	cervix:	n/a	n/a
47	BHLHE40	chr8:54754976-54756221	HepG2	liver:	n/a	chr8:54755915-54755931 chr8:54755842-54755855 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755866 chr8:54755859-54755868 chr8:54755844-54755853 chr8:54755852-54755873 chr8:54755843-54755852 chr8:54755858-54755867
48	RFX5	chr8:54756075-54756362	K562	blood:	n/a	n/a
49	MAX	chr8:54755296-54756251	H1-hESC	embryonic stem cell:	n/a	chr8:54755843-54755854 chr8:54755845-54755854 chr8:54755858-54755867 chr8:54755844-54755853 chr8:54755857-54755868 chr8:54755842-54755855 chr8:54755844-54755853
50	TCF7L2	chr8:54755245-54756263	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:54651332..54653261-chr8:54754407..54756402,2	MCF-7	breast:
2	chr8:54754073..54757431-chr8:54763114..54767534,4	K562	blood:
3	chr8:54755728..54757820-chr8:101732813..101735091,2	MCF-7	breast:
4	chr8:54755454..54757105-chr8:54791568..54794141,2	K562	blood:
5	chr8:54755685..54759999-chr8:54761654..54766287,5	MCF-7	breast:
6	chr1:11968133..11968902-chr8:54755086..54756316,3	HCT-116	colon:
7	chr8:54749963..54753631-chr8:54753914..54756219,5	MCF-7	breast:
8	chr8:54754942..54758152-chr8:54933404..54936388,3	K562	blood:
9	chr8:53624816..53627483-chr8:54753343..54757526,4	K562	blood:

Variant related genes	Relation type
ATP6V1H	TF binding region
ENSG00000199347	Chromatin interaction
ENSG00000187735	Chromatin interaction
ENSG00000147509	Chromatin interaction
ENSG00000023287	Chromatin interaction
ENSG00000047249	Chromatin interaction
ENSG00000070756	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004228	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10504158	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11985729	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1384797	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1483538	1.00[CEU][hapmap];0.97[GIH][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1483539	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[EUR][1000 genomes]
rs1483540	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1483542	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs16919616	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1842982	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1842983	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1842984	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2062226	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2306584	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306585	0.98[ASN][1000 genomes]
rs3824121	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57546155	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57553178	0.84[EUR][1000 genomes]
rs58652215	0.94[EUR][1000 genomes]
rs60696924	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60819522	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61194604	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61433056	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6473894	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs6994332	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6997050	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6998532	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7016171	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7017291	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7017967	0.94[EUR][1000 genomes]
rs73680325	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73680341	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73680342	0.94[EUR][1000 genomes]
rs73680346	0.84[EUR][1000 genomes]
rs7827611	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7831399	1.00[CEU][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54753400-54756600	Active TSS	Brain Anterior Caudate	brain
2	chr8:54753600-54756600	Active TSS	NHLF	lung
3	chr8:54753800-54756600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr8:54754000-54756400	Active TSS	Stomach Smooth Muscle	stomach
5	chr8:54754000-54756600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr8:54754000-54756600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:54754000-54756600	Active TSS	Colonic Mucosa	Colon
8	chr8:54754000-54756600	Active TSS	Fetal Intestine Small	intestine
9	chr8:54754200-54756400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:54754200-54756400	Active TSS	Brain Angular Gyrus	brain
11	chr8:54754200-54756400	Active TSS	Brain Hippocampus Middle	brain
12	chr8:54754200-54756400	Active TSS	NHDF-Ad	bronchial
13	chr8:54754200-54756600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr8:54754200-54756600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:54754200-54756600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:54754200-54756600	Active TSS	Fetal Intestine Large	intestine
17	chr8:54754200-54756600	Active TSS	K562	blood
18	chr8:54754200-54756800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr8:54754400-54756400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:54754400-54756400	Active TSS	HMEC	breast
21	chr8:54754400-54756400	Active TSS	NHEK	skin
22	chr8:54754400-54756600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr8:54754400-54756600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:54754400-54756600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr8:54754400-54756600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr8:54754400-54756600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:54754400-54756600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:54754400-54756600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr8:54754400-54756600	Active TSS	HSMMtube	muscle
30	chr8:54754400-54757200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:54754600-54756400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr8:54754600-54756400	Active TSS	Muscle Satellite Cultured Cells	--
33	chr8:54754600-54756400	Active TSS	Fetal Kidney	kidney
34	chr8:54754600-54756600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr8:54754600-54756600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr8:54754600-54756600	Active TSS	Fetal Brain Female	brain
37	chr8:54754600-54756600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr8:54754800-54756400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr8:54754800-54756400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:54754800-54756400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr8:54754800-54756400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:54754800-54756400	Active TSS	Brain Germinal Matrix	brain
43	chr8:54754800-54756400	Active TSS	Brain Substantia Nigra	brain
44	chr8:54754800-54756400	Active TSS	Colon Smooth Muscle	Colon
45	chr8:54754800-54756400	Active TSS	Fetal Muscle Trunk	muscle
46	chr8:54754800-54756400	Active TSS	Fetal Muscle Leg	muscle
47	chr8:54754800-54756400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr8:54754800-54756400	Active TSS	Small Intestine	intestine
49	chr8:54754800-54756400	Active TSS	Thymus	Thymus
50	chr8:54754800-54756400	Active TSS	Hela-S3	cervix

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