Variant report

Variant	rs442458
Chromosome Location	chr6:13712752-13712753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:173)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:173 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:13712168-13712789	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:13712131-13712847	HepG2	liver:	n/a	n/a
3	FOXM1	chr6:13712093-13712805	GM12878	blood:	n/a	n/a
4	REST	chr6:13712046-13712800	HL-60	blood:	n/a	n/a
5	SPI1	chr6:13712586-13713446	GM12878	blood:	n/a	chr6:13712763-13712776
6	CBX3	chr6:13712182-13713153	K562	blood:	n/a	n/a
7	IKZF1	chr6:13712749-13713130	GM12878	blood:	n/a	n/a
8	FOXM1	chr6:13712189-13713035	GM12878	blood:	n/a	n/a
9	ZNF143	chr6:13712147-13712782	Hela-S3	cervix:	n/a	n/a
10	RFX5	chr6:13711912-13713126	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:13711660-13712767	GM12891	blood:	n/a	n/a
12	EP300	chr6:13712213-13712876	GM12878	blood:	n/a	chr6:13712435-13712444 chr6:13712295-13712304
13	MAFK	chr6:13712306-13713097	Hela-S3	cervix:	n/a	chr6:13713041-13713056
14	POLR2A	chr6:13711608-13713176	K562	blood:	n/a	n/a
15	TCF12	chr6:13712112-13712753	ECC-1	luminal epithelium:	n/a	n/a
16	MXI1	chr6:13711636-13713082	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:13710881-13712994	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:13711507-13713041	K562	blood:	n/a	n/a
19	RCOR1	chr6:13711878-13712824	Hela-S3	cervix:	n/a	n/a
20	MAX	chr6:13711491-13712824	HepG2	liver:	n/a	n/a
21	EP300	chr6:13712261-13713240	GM12878	blood:	n/a	chr6:13712435-13712444 chr6:13712295-13712304
22	POLR2A	chr6:13711499-13712767	HUVEC	blood vessel:	n/a	n/a
23	MAX	chr6:13711584-13712785	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr6:13711498-13712889	HUVEC	blood vessel:	n/a	n/a
25	TBL1XR1	chr6:13711811-13713076	K562	blood:	n/a	n/a
26	POLR2A	chr6:13711423-13712769	ProgFib	skin:	n/a	n/a
27	ARID3A	chr6:13712424-13713017	K562	blood:	n/a	chr6:13712676-13712692
28	MBD4	chr6:13712161-13712943	HepG2	liver:	n/a	n/a
29	TBP	chr6:13712273-13713163	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr6:13712344-13712992	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr6:13712186-13713171	GM12878	blood:	n/a	n/a
32	TBP	chr6:13712235-13713175	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:13711521-13712798	K562	blood:	n/a	n/a
34	MAFK	chr6:13712149-13713121	IMR90	lung:	n/a	chr6:13713041-13713056
35	EP300	chr6:13711700-13713101	K562	blood:	n/a	chr6:13712034-13712043 chr6:13712435-13712444 chr6:13712295-13712304 chr6:13711814-13711823
36	POLR2A	chr6:13711513-13712830	PFSK-1	brain:	n/a	n/a
37	NR2F2	chr6:13712036-13713392	K562	blood:	n/a	n/a
38	POLR2A	chr6:13712154-13713161	SK-N-MC	brain:	n/a	n/a
39	MAX	chr6:13711541-13712839	HepG2	liver:	n/a	n/a
40	TAF1	chr6:13711510-13712765	K562	blood:	n/a	n/a
41	POLR2A	chr6:13711640-13713056	K562	blood:	n/a	n/a
42	CHD1	chr6:13711607-13713115	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:13712038-13712759	SK-N-SH	brain:	n/a	n/a
44	MAX	chr6:13711607-13712830	HCT-116	colon:	n/a	n/a
45	PML	chr6:13711478-13712810	GM12878	blood:	n/a	n/a
46	GATA3	chr6:13712654-13713332	T-47D	breast:	n/a	n/a
47	NRF1	chr6:13711860-13712947	SK-N-SH	brain:	n/a	n/a
48	MAX	chr6:13711656-13712799	MCF-7	breast:	n/a	n/a
49	MAX	chr6:13712112-13712784	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:13712150-13712831	U87	brain:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13686589..13691071-chr6:13710597..13713720,6	K562	blood:
2	chr6:13703743..13705757-chr6:13712344..13714353,2	MCF-7	breast:
3	chr6:13612439..13617063-chr6:13710643..13713872,7	MCF-7	breast:
4	chr6:13685654..13687254-chr6:13711731..13713330,2	MCF-7	breast:
5	chr3:5028007..5028637-chr6:13712568..13713098,2	Hela-S3	cervix:
6	chr6:13712256..13714398-chr6:13725384..13727195,2	MCF-7	breast:
7	chr6:13710342..13712818-chr6:13812780..13815719,5	MCF-7	breast:
8	chr6:13613792..13617654-chr6:13711804..13714048,3	K562	blood:
9	chr6:13712562..13715550-chr6:13731027..13734094,5	K562	blood:
10	chr12:120729387..120731467-chr6:13710748..13713061,2	MCF-7	breast:
11	chr6:13712294..13715235-chr6:13734842..13736345,2	K562	blood:
12	chr6:13612229..13617961-chr6:13707977..13713490,13	K562	blood:
13	chr6:13658437..13687167-chr6:13707669..13717356,51	K562	blood:
14	chr6:13272896..13275816-chr6:13711430..13713666,2	K562	blood:
15	chr6:13613655..13618769-chr6:13709987..13714197,10	MCF-7	breast:
16	chr6:13711887..13713957-chr6:13747635..13751147,3	K562	blood:
17	chr6:13617821..13621321-chr6:13710420..13713075,4	MCF-7	breast:
18	chr6:13712335..13712843-chr6:13813904..13814896,2	NB4	blood:
19	chr6:13712160..13713873-chr6:13816640..13818344,2	K562	blood:
20	chr6:13710378..13713685-chr6:13811318..13818372,10	MCF-7	breast:
21	chr6:13573088..13576408-chr6:13709684..13713261,5	MCF-7	breast:
22	chr6:13573221..13576787-chr6:13710917..13713733,6	K562	blood:
23	chr6:13711847..13714774-chr6:13741208..13742857,2	K562	blood:
24	chr6:13677099..13683232-chr6:13708060..13717356,16	K562	blood:
25	chr1:65532144..65534298-chr6:13711181..13713399,2	MCF-7	breast:
26	chr6:13573217..13575552-chr6:13711779..13713289,2	K562	blood:
27	chr6:13709898..13716469-chr6:13809605..13815390,11	K562	blood:

No data

Variant related genes	Relation type
RANBP9	TF binding region
ENSG00000261071	Chromatin interaction
ENSG00000112137	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000231485	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000252966	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000268059	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000050393	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000233075	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456703	0.85[ASN][1000 genomes]
rs169461	0.94[CHB][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs204224	0.82[ASN][1000 genomes]
rs204231	0.84[GIH][hapmap]
rs204233	0.85[ASN][1000 genomes]
rs204234	0.85[ASN][1000 genomes]
rs204235	0.85[ASN][1000 genomes]
rs204236	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs204237	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs204238	0.85[ASN][1000 genomes]
rs204239	0.85[ASN][1000 genomes]
rs204240	0.86[ASN][1000 genomes]
rs204242	0.86[ASN][1000 genomes]
rs3752502	0.94[CHB][hapmap];0.92[GIH][hapmap]
rs379844	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs411094	0.99[ASN][1000 genomes]
rs59313939	0.83[ASN][1000 genomes]
rs6927142	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9382329	0.94[CHB][hapmap];0.92[GIH][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	74 gene(s)	inside rSNPs	diseases
2	nsv883451	chr6:13704341-13728670	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv883452	chr6:13704341-13733565	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	esv3404065	chr6:13709573-13714171	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv3387564	chr6:13710598-13713146	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3361820	chr6:13710773-13713121	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13707800-13713000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:13708400-13713000	Active TSS	HSMMtube	muscle
3	chr6:13708400-13713200	Active TSS	NHLF	lung
4	chr6:13708600-13712800	Active TSS	Esophagus	oesophagus
5	chr6:13708600-13712800	Active TSS	Stomach Smooth Muscle	stomach
6	chr6:13708600-13713000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:13708600-13713000	Active TSS	Brain Anterior Caudate	brain
8	chr6:13708600-13713000	Active TSS	Colonic Mucosa	Colon
9	chr6:13708600-13713200	Active TSS	Brain Angular Gyrus	brain
10	chr6:13708800-13712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:13708800-13712800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:13708800-13712800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:13708800-13712800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:13708800-13712800	Active TSS	Fetal Kidney	kidney
15	chr6:13708800-13713000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:13708800-13713000	Active TSS	Fetal Intestine Large	intestine
17	chr6:13708800-13713000	Active TSS	Fetal Stomach	stomach
18	chr6:13708800-13713200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:13708800-13713200	Active TSS	Ovary	ovary
20	chr6:13709000-13712800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:13709000-13713000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:13709000-13713000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:13709000-13713000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr6:13709000-13713000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:13709000-13713000	Active TSS	Placenta	Placenta
26	chr6:13709000-13713000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:13709000-13713200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:13709000-13713200	Active TSS	Fetal Intestine Small	intestine
29	chr6:13709000-13713200	Active TSS	Psoas Muscle	Psoas
30	chr6:13709200-13712800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:13709200-13712800	Active TSS	Primary T cells fromperipheralblood	blood
32	chr6:13709200-13712800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:13709200-13712800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:13709200-13712800	Active TSS	Fetal Thymus	thymus
35	chr6:13709200-13713000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:13709200-13713000	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:13709200-13713000	Active TSS	Colon Smooth Muscle	Colon
38	chr6:13709200-13713000	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:13709200-13713200	Active TSS	Aorta	Aorta
40	chr6:13709200-13713200	Active TSS	Right Ventricle	heart
41	chr6:13709600-13712800	Active TSS	Brain Substantia Nigra	brain
42	chr6:13709600-13713000	Active TSS	Fetal Lung	lung
43	chr6:13709600-13713000	Active TSS	Rectal Smooth Muscle	rectum
44	chr6:13709600-13713200	Active TSS	A549	lung
45	chr6:13709800-13712800	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:13709800-13713000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr6:13709800-13713200	Active TSS	H1 Cell Line	embryonic stem cell
48	chr6:13710000-13712800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:13710000-13712800	Active TSS	Lung	lung
50	chr6:13710000-13712800	Active TSS	Pancreas	Pancrea

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