Variant report

Variant	rs2841523
Chromosome Location	chr6:13613783-13613784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr6:13613527-13614070	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:13613293-13616542	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:13613565-13614055	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:13613652-13614026	MCF-7	breast:	n/a	n/a
5	POLR2A	chr6:13613120-13613962	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr6:13613363-13618463	K562	blood:	n/a	n/a
7	RAD21	chr6:13613558-13613786	HepG2	liver:	n/a	chr6:13613619-13613638
8	POLR2A	chr6:13613352-13614133	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:13613746-13613851	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr6:13613179-13613783	K562	blood:	n/a	n/a
11	POLR2A	chr6:13613512-13614061	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr6:13613634-13616783	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr6:13612829-13613952	Raji	blood:	n/a	n/a
14	POLR2A	chr6:13613290-13618341	HepG2	liver:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13602809..13604762-chr6:13612236..13614334,2	MCF-7	breast:
2	chr6:13590020..13592092-chr6:13613301..13614850,2	MCF-7	breast:
3	chr6:13613755..13617282-chr6:13813110..13815971,5	MCF-7	breast:
4	chr6:13613655..13618769-chr6:13709987..13714197,10	MCF-7	breast:
5	chr6:13592972..13596401-chr6:13611564..13614564,3	K562	blood:
6	chr6:13572865..13577994-chr6:13612366..13619020,17	K562	blood:
7	chr6:13572710..13576955-chr6:13610549..13618685,22	MCF-7	breast:
8	chr6:13550240..13552632-chr6:13612662..13615380,2	K562	blood:
9	chr17:56735175..56738021-chr6:13613388..13615858,2	MCF-7	breast:
10	chr6:13611124..13612865-chr6:13613268..13615090,3	MCF-7	breast:
11	chr6:13612439..13617063-chr6:13710643..13713872,7	MCF-7	breast:
12	chr6:13584952..13586852-chr6:13613634..13615316,2	K562	blood:
13	chr6:13486545..13489203-chr6:13612282..13616748,6	MCF-7	breast:
14	chr6:13604364..13607070-chr6:13613541..13615368,4	K562	blood:
15	chr6:13612229..13617961-chr6:13707977..13713490,13	K562	blood:
16	chr6:13613412..13615383-chr6:13705399..13707635,2	K562	blood:
17	chr6:13550897..13553809-chr6:13613008..13614749,2	MCF-7	breast:
18	chr6:13612983..13618304-chr6:13679034..13683117,5	K562	blood:
19	chr6:13612104..13613937-chr6:13641245..13643744,2	K562	blood:

No data

Variant related genes	Relation type
NOL7	TF binding region
ENSG00000010017	Chromatin interaction
ENSG00000050393	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000252966	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10807467	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11962124	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12209803	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]
rs12664567	0.87[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2253217	0.85[YRI][hapmap]
rs2841514	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2841515	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841517	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841518	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841520	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2841521	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2841522	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2841524	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757260	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800503	0.96[CEU][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3823453	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745101	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760411	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2841523	HIVEP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13575600-13613800	Weak transcription	Stomach Mucosa	stomach
2	chr6:13575600-13614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:13575800-13614200	Weak transcription	HUVEC	blood vessel
4	chr6:13575800-13614600	Weak transcription	Right Atrium	heart
5	chr6:13576200-13614400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:13580400-13614800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:13585600-13613800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:13588400-13614200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:13588600-13614000	Weak transcription	NHLF	lung
10	chr6:13588600-13614400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:13588800-13614600	Weak transcription	Small Intestine	intestine
12	chr6:13589000-13614400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:13595600-13614600	Weak transcription	Thymus	Thymus
14	chr6:13595600-13614800	Weak transcription	Aorta	Aorta
15	chr6:13597200-13613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:13597200-13614400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:13597200-13614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:13597600-13613800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:13597600-13614400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:13597600-13614400	Weak transcription	Fetal Lung	lung
21	chr6:13598600-13614400	Weak transcription	Fetal Kidney	kidney
22	chr6:13599400-13614400	Weak transcription	Esophagus	oesophagus
23	chr6:13599400-13614800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:13599600-13614800	Weak transcription	Gastric	stomach
25	chr6:13601400-13614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:13601400-13614400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:13601600-13614400	Weak transcription	Colonic Mucosa	Colon
28	chr6:13601600-13614400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:13601600-13614400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:13601600-13614400	Weak transcription	Right Ventricle	heart
31	chr6:13601600-13614400	Weak transcription	Spleen	Spleen
32	chr6:13601600-13614800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:13601800-13613800	Weak transcription	HMEC	breast
34	chr6:13601800-13613800	Weak transcription	NHEK	skin
35	chr6:13601800-13614400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:13602200-13614000	Weak transcription	HSMMtube	muscle
37	chr6:13602200-13614400	Weak transcription	Brain Germinal Matrix	brain
38	chr6:13602400-13614400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:13602400-13614400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:13602400-13614600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:13603000-13614400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:13603000-13614400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:13603000-13614400	Weak transcription	Primary T cells from cord blood	blood
44	chr6:13604000-13614200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:13604200-13613800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:13604800-13614400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:13605000-13614400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:13605200-13614400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:13605400-13614000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:13605400-13614400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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