Variant report

Variant	rs12209803
Chromosome Location	chr6:13623324-13623325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13621910-13623840	K562	blood:	n/a	n/a
2	POLR2A	chr6:13623014-13623442	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:13620335-13625596	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:13618693-13627590	K562	blood:	n/a	n/a
5	POLR2A	chr6:13622313-13623847	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:13621964-13623911	GM12891	blood:	n/a	n/a
7	POLR2A	chr6:13623153-13623338	K562	blood:	n/a	n/a
8	POLR2A	chr6:13622430-13623365	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr6:13623185-13623384	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr6:13623035-13623332	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:13623094-13623407	HL-60	blood:	n/a	n/a
12	CUX1	chr6:13623307-13623692	K562	blood:	n/a	chr6:13623502-13623511
13	POLR2A	chr6:13622982-13623358	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:13623013-13623973	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:13623044-13623622	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr6:13622996-13623419	MCF-7	breast:	n/a	n/a
17	POLR2A	chr6:13621729-13623872	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:13622429-13623345	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13621813..13624606-chr6:13711538..13713160,2	MCF-7	breast:
2	chr6:13621337..13626470-chr6:13709829..13716449,7	K562	blood:
3	chr6:13614941..13617612-chr6:13622081..13626001,4	MCF-7	breast:
4	chr6:13622245..13624613-chr6:13641011..13644598,3	K562	blood:
5	chr6:13622285..13628716-chr6:13632838..13638490,8	K562	blood:
6	chr6:13621845..13624012-chr6:13637610..13640298,2	MCF-7	breast:
7	chr6:13622436..13626191-chr6:13709343..13710896,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268059	TF binding region
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10807467	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948804	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11962124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253217	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs2841514	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2841515	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2841517	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2841518	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2841520	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2841521	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2841522	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2841523	0.87[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2841524	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3757260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800503	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823453	0.96[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6899402	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7745101	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7760411	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][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	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	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209803	HIVEP1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13616600-13624200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:13616600-13637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:13617000-13628200	Strong transcription	Fetal Muscle Leg	muscle
4	chr6:13617000-13633000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr6:13617200-13623400	Strong transcription	Fetal Stomach	stomach
6	chr6:13617200-13623600	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr6:13617200-13623800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr6:13617200-13624000	Strong transcription	Brain Anterior Caudate	brain
9	chr6:13617200-13624600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:13617200-13625000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:13617200-13626000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:13617200-13627200	Strong transcription	NH-A	brain
13	chr6:13617200-13627600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:13617200-13632800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:13617200-13632800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr6:13617200-13633800	Weak transcription	Stomach Mucosa	stomach
17	chr6:13617200-13634600	Strong transcription	Placenta	Placenta
18	chr6:13617200-13634800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:13617200-13634800	Strong transcription	Fetal Intestine Large	intestine
20	chr6:13617200-13638800	Weak transcription	Aorta	Aorta
21	chr6:13617400-13625400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:13617400-13625400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:13617400-13625600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:13617400-13627600	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr6:13617400-13627600	Strong transcription	HSMMtube	muscle
26	chr6:13617400-13630400	Strong transcription	Primary B cells from cord blood	blood
27	chr6:13617400-13636400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:13617600-13624000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:13617600-13626000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:13617600-13626000	Strong transcription	NHEK	skin
31	chr6:13617600-13627000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:13617600-13627400	Strong transcription	Left Ventricle	heart
33	chr6:13617600-13627600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:13617600-13627800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:13617600-13632000	Strong transcription	Adipose Nuclei	Adipose
36	chr6:13617600-13632800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:13617600-13633000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:13617600-13634600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:13617600-13634800	Strong transcription	Primary T cells from cord blood	blood
40	chr6:13617600-13635400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:13617600-13642200	Strong transcription	Fetal Thymus	thymus
42	chr6:13617600-13642200	Strong transcription	HSMM	muscle
43	chr6:13617600-13642400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:13617800-13623400	Strong transcription	Ovary	ovary
45	chr6:13617800-13623600	Strong transcription	Brain Substantia Nigra	brain
46	chr6:13617800-13623800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr6:13617800-13625200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:13617800-13625600	Strong transcription	NHLF	lung
49	chr6:13617800-13627200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr6:13617800-13627800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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