Variant report

Variant	rs9403384
Chromosome Location	chr6:142709601-142709602
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	CTCF	chr6:142709480-142709630	AG04449	skin:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
2	CTCF	chr6:142709467-142709682	A549	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
3	CTCF	chr6:142709480-142709630	AG04450	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
4	CTCF	chr6:142709460-142709610	HFF-Myc	foreskin:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
5	CEBPB	chr6:142709153-142709705	Hela-S3	cervix:	n/a	chr6:142709477-142709490 chr6:142709477-142709490 chr6:142709478-142709489 chr6:142709477-142709488 chr6:142709477-142709488 chr6:142709477-142709490
6	CTCF	chr6:142709480-142709630	GM12874	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
7	CTCF	chr6:142709318-142709717	MCF-7	breast:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
8	CTCF	chr6:142709460-142709610	SK-N-SH_RA	brain:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
9	CTCF	chr6:142709520-142709670	GM12872	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
10	CTCF	chr6:142709480-142709630	AG09309	skin:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
11	CTCF	chr6:142709446-142709648	Lung_OC	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
12	RAD21	chr6:142709304-142709770	A549	lung:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
13	CTCF	chr6:142709430-142709683	Hela-S3	cervix:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
14	CTCF	chr6:142709456-142709658	K562	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
15	CTCF	chr6:142709500-142709650	GM12873	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
16	RAD21	chr6:142709357-142709731	H1-hESC	embryonic stem cell:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
17	CTCF	chr6:142709480-142709630	NHDF-neo	bronchial:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
18	CEBPB	chr6:142709306-142709670	HepG2	liver:	n/a	chr6:142709477-142709490 chr6:142709477-142709490 chr6:142709478-142709489 chr6:142709477-142709488 chr6:142709477-142709488 chr6:142709477-142709490
19	CTCF	chr6:142709369-142709759	GM12878	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
20	CTCF	chr6:142709500-142709650	GM12878	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
21	CTCF	chr6:142709485-142709676	Gliobla	brain:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
22	CTCF	chr6:142709480-142709630	BJ	skin:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
23	CTCF	chr6:142709460-142709610	Hela-S3	cervix:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
24	CTCF	chr6:142709460-142709610	WERI-Rb-1	eye:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
25	RAD21	chr6:142709197-142709756	HepG2	liver:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
26	RAD21	chr6:142709242-142709769	IMR90	lung:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
27	CTCF	chr6:142709364-142709753	IMR90	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
28	CTCF	chr6:142709480-142709630	HepG2	liver:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
29	STAT3	chr6:142709402-142709610	MCF10A-Er-Src	breast:	n/a	n/a
30	BCL3	chr6:142709205-142709630	A549	lung:	n/a	n/a
31	CTCF	chr6:142709500-142709650	AG09319	gingival:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
32	CTCF	chr6:142709502-142709631	GM13976	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
33	CTCF	chr6:142709460-142709610	AG04450	lung:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
34	ARID3A	chr6:142709364-142709680	HepG2	liver:	n/a	n/a
35	SMC3	chr6:142709456-142709656	K562	blood:	n/a	chr6:142709541-142709555
36	MAX	chr6:142709456-142709835	A549	lung:	n/a	n/a
37	FOXA1	chr6:142709176-142709761	HepG2	liver:	n/a	n/a
38	CTCF	chr6:142709500-142709650	HRE	kidney:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
39	CTCF	chr6:142709445-142709675	Pancreas_OC	pancreas:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
40	CTCF	chr6:142709480-142709630	HCPEpiC	choroid plexus:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
41	CTCF	chr6:142709496-142709648	MCF-7	breast:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
42	SMC3	chr6:142709169-142709975	SK-N-SH	brain:	n/a	chr6:142709541-142709555
43	CTCF	chr6:142709480-142709630	AG10803	skin:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
44	CTCF	chr6:142709480-142709630	HEK293	kidney:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
45	CTCF	chr6:142709480-142709630	Hela-S3	cervix:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
46	RAD21	chr6:142709407-142709822	MCF-7	breast:	n/a	chr6:142709547-142709554 chr6:142709537-142709556
47	CEBPB	chr6:142709341-142709628	K562	blood:	n/a	chr6:142709477-142709490 chr6:142709477-142709490 chr6:142709478-142709489 chr6:142709477-142709488 chr6:142709477-142709488 chr6:142709477-142709490
48	ZNF143	chr6:142709413-142709705	GM12878	blood:	n/a	n/a
49	CTCF	chr6:142709480-142709630	HPAF	blood vessel:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555
50	CTCF	chr6:142709520-142709670	GM12868	blood:	n/a	chr6:142709539-142709557 chr6:142709544-142709552 chr6:142709534-142709555

No.	Distal block	Cell Line	Cell type
1	chr6:142477371..142478101-chr6:142709070..142709995,3	K562	blood:
2	chr6:142596671..142598809-chr6:142708125..142710238,2	MCF-7	breast:
3	chr6:142467634..142468596-chr6:142709170..142710030,4	MCF-7	breast:
4	chr6:142621739..142624319-chr6:142709513..142711217,3	MCF-7	breast:
5	chr6:142466930..142469707-chr6:142709065..142710643,2	K562	blood:
6	chr6:142528358..142528953-chr6:142709482..142710029,2	MCF-7	breast:
7	chr6:142616281..142618889-chr6:142707145..142709982,2	MCF-7	breast:

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000112414	Chromatin interaction
ENSG00000009844	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1013902	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071798	0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064314	0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2143390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223616	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294765	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294768	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294770	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294772	0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294773	1.00[ASW][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294774	0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34701089	0.86[EUR][1000 genomes]
rs41289839	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140531	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570512	0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6913116	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7758750	0.88[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759268	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321865	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321871	0.83[EUR][1000 genomes]
rs9373343	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373345	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376687	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9376689	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385993	0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9385994	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389988	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9389990	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403379	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9484645	0.86[EUR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:142700000-142714200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:142705800-142713800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:142706200-142719600	Weak transcription	NHEK	skin
7	chr6:142706400-142717200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:142706600-142710200	Enhancers	A549	lung
9	chr6:142706800-142709800	Weak transcription	HSMM	muscle
10	chr6:142707800-142709800	Genic enhancers	HepG2	liver
11	chr6:142708000-142710000	Enhancers	Liver	Liver
12	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
13	chr6:142708200-142710000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:142708200-142710000	Enhancers	NHLF	lung
15	chr6:142708200-142718600	Weak transcription	Placenta	Placenta
16	chr6:142708200-142719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:142708800-142711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:142709200-142709800	Enhancers	Brain Hippocampus Middle	brain
19	chr6:142709200-142710000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:142709200-142710000	Enhancers	HUVEC	blood vessel
21	chr6:142709200-142710600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:142709200-142721000	Weak transcription	Fetal Intestine Small	intestine
23	chr6:142709400-142711800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:142709400-142718800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:142709600-142709800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:142709600-142709800	Enhancers	Fetal Kidney	kidney
27	chr6:142709600-142709800	Flanking Active TSS	Fetal Lung	lung
28	chr6:142709600-142710000	Enhancers	Primary T cells from cord blood	blood

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