Variant report

Variant	rs2841524
Chromosome Location	chr6:13615401-13615402
allele	A/C
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	SP4	chr6:13614980-13615871	H1-hESC	embryonic stem cell:	n/a	chr6:13615447-13615463
2	POLR2A	chr6:13615004-13615938	GM12878	blood:	n/a	n/a
3	CTCF	chr6:13615251-13615710	A549	lung:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
4	POLR2A	chr6:13615009-13615862	GM12891	blood:	n/a	n/a
5	MAX	chr6:13614899-13615758	A549	lung:	n/a	chr6:13615415-13615425 chr6:13614932-13614942 chr6:13615415-13615425 chr6:13615414-13615427 chr6:13615415-13615426
6	POLR2A	chr6:13615028-13615902	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:13614447-13616555	HepG2	liver:	n/a	n/a
8	CBX3	chr6:13614681-13615901	K562	blood:	n/a	n/a
9	POLR2A	chr6:13614344-13616751	IMR90	lung:	n/a	n/a
10	GABPA	chr6:13615069-13616110	A549	lung:	n/a	chr6:13615469-13615483 chr6:13615469-13615480 chr6:13615471-13615480 chr6:13615466-13615480 chr6:13615469-13615478
11	NR2F2	chr6:13615045-13616058	MCF-7	breast:	n/a	chr6:13615552-13615567
12	REST	chr6:13615222-13615577	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr6:13615101-13615829	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr6:13614572-13616292	Hela-S3	cervix:	n/a	n/a
15	EGR1	chr6:13615271-13615795	K562	blood:	n/a	chr6:13615470-13615479
16	POLR2A	chr6:13614861-13616174	Gliobla	brain:	n/a	n/a
17	SIN3AK20	chr6:13614743-13616329	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr6:13614815-13616211	GM15510	blood:	n/a	n/a
19	MXI1	chr6:13614629-13616324	GM12878	blood:	n/a	chr6:13615415-13615424 chr6:13615415-13615424
20	SIX5	chr6:13615334-13615623	K562	blood:	n/a	n/a
21	SIN3AK20	chr6:13615247-13615672	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr6:13615358-13615659	Pancreas_OC	pancreas:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
23	RELA	chr6:13614954-13615870	GM15510	blood:	n/a	n/a
24	CTCF	chr6:13615360-13615653	LNCaP	prostate:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
25	CTCF	chr6:13615400-13615550	WI-38	lung:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
26	CTCF	chr6:13615176-13615746	K562	blood:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
27	CTCF	chr6:13615295-13615720	MCF-7	breast:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
28	POLR2A	chr6:13614267-13616296	MCF10A-Er-Src	breast:	n/a	n/a
29	GABPA	chr6:13615288-13615932	Hela-S3	cervix:	n/a	chr6:13615469-13615483 chr6:13615469-13615480 chr6:13615471-13615480 chr6:13615466-13615480 chr6:13615469-13615478
30	STAT5A	chr6:13614738-13616126	GM12878	blood:	n/a	chr6:13615459-13615467 chr6:13615259-13615270
31	RUNX3	chr6:13614689-13615914	GM12878	blood:	n/a	n/a
32	SIN3A	chr6:13614446-13616468	H1-hESC	embryonic stem cell:	n/a	chr6:13615415-13615424
33	ZMIZ1	chr6:13615216-13616288	K562	blood:	n/a	n/a
34	ELF1	chr6:13614753-13616135	GM12878	blood:	n/a	chr6:13615549-13615558 chr6:13614967-13614979 chr6:13615548-13615559
35	GABPA	chr6:13615152-13615941	A549	lung:	n/a	chr6:13615469-13615483 chr6:13615469-13615480 chr6:13615471-13615480 chr6:13615466-13615480 chr6:13615469-13615478
36	PML	chr6:13614931-13615877	MCF-7	breast:	n/a	n/a
37	PML	chr6:13614991-13615922	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:13614798-13616423	H1-neurons	neurons:	n/a	n/a
39	ATF2	chr6:13615084-13615697	H1-hESC	embryonic stem cell:	n/a	n/a
40	NRF1	chr6:13615180-13615747	GM12878	blood:	n/a	chr6:13615468-13615479 chr6:13615469-13615483 chr6:13615469-13615480 chr6:13615471-13615480 chr6:13615466-13615480 chr6:13615469-13615478
41	POLR2A	chr6:13614809-13616538	SK-N-SH	brain:	n/a	n/a
42	MYC	chr6:13615095-13615825	MCF-7	breast:	n/a	chr6:13615415-13615425 chr6:13615415-13615425 chr6:13615414-13615427 chr6:13615415-13615426
43	POLR2A	chr6:13614663-13615982	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr6:13615400-13615550	GM12870	blood:	n/a	chr6:13615502-13615520 chr6:13615504-13615512
45	USF1	chr6:13615199-13615719	A549	lung:	n/a	chr6:13615414-13615425
46	REST	chr6:13615101-13615807	PFSK-1	brain:	n/a	n/a
47	MAZ	chr6:13614810-13616342	K562	blood:	n/a	chr6:13615414-13615427 chr6:13615415-13615425 chr6:13615415-13615426 chr6:13615415-13615425 chr6:13614932-13614942
48	TAF1	chr6:13614818-13616049	ECC-1	luminal epithelium:	n/a	n/a
49	ATF3	chr6:13615213-13615629	K562	blood:	n/a	n/a
50	E2F4	chr6:13614779-13616331	K562	blood:	n/a	chr6:13615470-13615479

No.	Distal block	Cell Line	Cell type
1	chr16:88877881..88878573-chr6:13614748..13615603,2	Hela-S3	cervix:
2	chr6:13613755..13617282-chr6:13813110..13815971,5	MCF-7	breast:
3	chr6:13572923..13577086-chr6:13614342..13617597,6	K562	blood:
4	chr6:13613655..13618769-chr6:13709987..13714197,10	MCF-7	breast:
5	chr6:13615100..13618262-chr6:13632919..13636030,3	K562	blood:
6	chr11:65382317..65383070-chr6:13615130..13615823,2	Hela-S3	cervix:
7	chr12:121341724..121342252-chr6:13615154..13615782,2	Hela-S3	cervix:
8	chr6:13572865..13577994-chr6:13612366..13619020,17	K562	blood:
9	chr6:13573004..13578027-chr6:13613856..13617870,10	MCF-7	breast:
10	chr6:13572710..13576955-chr6:13610549..13618685,22	MCF-7	breast:
11	chr6:13486736..13489619-chr6:13614070..13616875,2	MCF-7	breast:
12	chr17:56735175..56738021-chr6:13613388..13615858,2	MCF-7	breast:
13	chr12:50134932..50135758-chr6:13615043..13615660,2	Hela-S3	cervix:
14	chr6:13612439..13617063-chr6:13710643..13713872,7	MCF-7	breast:
15	chr6:13614758..13615482-chr6:43737724..43738442,2	Hela-S3	cervix:
16	chr6:13486545..13489203-chr6:13612282..13616748,6	MCF-7	breast:
17	chr6:13328551..13330063-chr6:13614830..13616645,2	MCF-7	breast:
18	chr15:44084317..44085015-chr6:13615250..13615759,2	Hela-S3	cervix:
19	chr6:13612229..13617961-chr6:13707977..13713490,13	K562	blood:
20	chr6:13408206..13410464-chr6:13614798..13617307,2	MCF-7	breast:
21	chr6:13614163..13617329-chr6:13617495..13621513,6	MCF-7	breast:
22	chr6:13486147..13488786-chr6:13613803..13616517,3	K562	blood:
23	chr6:13327180..13330479-chr6:13614329..13617751,5	MCF-7	breast:
24	chr6:13612983..13618304-chr6:13679034..13683117,5	K562	blood:

Variant related genes	Relation type
NOL7	TF binding region
ENSG00000261071	TF binding region
ENSG00000010017	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000252966	Chromatin interaction
ENSG00000268059	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000157837	Chromatin interaction
ENSG00000198931	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000050393	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10807467	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948804	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11962124	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209803	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]
rs12664567	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2841514	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2841515	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841517	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841518	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841520	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2841521	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841522	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841523	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];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3800503	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3823453	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899402	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745101	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7760411	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[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
rs2841524	HIVEP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13613400-13616600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:13613800-13616800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:13614000-13616800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:13614000-13617000	Active TSS	A549	lung
5	chr6:13614200-13616400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:13614200-13616600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:13614200-13616600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:13614400-13615600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr6:13614400-13616400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:13614400-13616400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:13614400-13616400	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:13614400-13616400	Active TSS	Brain Hippocampus Middle	brain
13	chr6:13614400-13616400	Active TSS	Pancreas	Pancrea
14	chr6:13614400-13616600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:13614400-13616600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:13614400-13616600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:13614400-13616600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:13614400-13616600	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:13614400-13617000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:13614400-13617000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:13614400-13617000	Active TSS	Fetal Kidney	kidney
22	chr6:13614400-13617000	Active TSS	HSMMtube	muscle
23	chr6:13614600-13616200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:13614600-13616200	Active TSS	Small Intestine	intestine
25	chr6:13614600-13616400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:13614600-13616400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:13614600-13616400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:13614600-13616400	Active TSS	Brain Angular Gyrus	brain
29	chr6:13614600-13616400	Active TSS	Brain Anterior Caudate	brain
30	chr6:13614600-13616400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:13614600-13616400	Active TSS	Fetal Intestine Large	intestine
32	chr6:13614600-13616400	Active TSS	Fetal Intestine Small	intestine
33	chr6:13614600-13616400	Active TSS	Fetal Stomach	stomach
34	chr6:13614600-13616400	Active TSS	Psoas Muscle	Psoas
35	chr6:13614600-13616400	Active TSS	Hela-S3	cervix
36	chr6:13614600-13616400	Active TSS	NH-A	brain
37	chr6:13614600-13616600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr6:13614600-13616600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:13614600-13616600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:13614600-13616600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:13614600-13616600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:13614600-13616600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:13614600-13616600	Active TSS	Esophagus	oesophagus
44	chr6:13614600-13616600	Active TSS	GM12878-XiMat	blood
45	chr6:13614600-13616800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:13614600-13616800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:13614600-13616800	Active TSS	HSMM	muscle
48	chr6:13614600-13617000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:13614600-13617000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:13614600-13617000	Active TSS	Left Ventricle	heart

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