Variant report

Variant	rs2747429
Chromosome Location	chr6:29648377-29648378
allele	C/T
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	POLR2A	chr6:29648334-29648564	GM12891	blood:	n/a	n/a
2	CTCF	chr6:29648280-29648430	HBMEC	blood vessel:	n/a	chr6:29648349-29648358
3	CTCF	chr6:29648280-29648430	GM12871	blood:	n/a	chr6:29648349-29648358
4	CTCF	chr6:29648300-29648450	GM12871	blood:	n/a	chr6:29648349-29648358
5	POLR2A	chr6:29648195-29649120	GM18951	blood:	n/a	n/a
6	CTCF	chr6:29648280-29648430	HMEC	breast:	n/a	chr6:29648349-29648358
7	CTCF	chr6:29648320-29648470	RPTEC	kidney:	n/a	chr6:29648349-29648358
8	CTCF	chr6:29648320-29648470	NHEK	skin:	n/a	chr6:29648349-29648358
9	CTCFL	chr6:29648265-29648412	K562	blood:	n/a	n/a
10	CTCF	chr6:29648280-29648430	WERI-Rb-1	eye:	n/a	chr6:29648349-29648358
11	YY1	chr6:29647863-29648474	GM12891	blood:	n/a	chr6:29648056-29648066 chr6:29648059-29648067 chr6:29648251-29648259
12	CTCF	chr6:29648320-29648470	MCF-7	breast:	n/a	chr6:29648349-29648358
13	CTCF	chr6:29648280-29648430	HCM	heart:	n/a	chr6:29648349-29648358
14	CTCF	chr6:29648260-29648410	NB4	blood:	n/a	chr6:29648349-29648358
15	CTCF	chr6:29648340-29648490	GM12878	blood:	n/a	chr6:29648349-29648358
16	POLR2A	chr6:29647749-29649223	GM12891	blood:	n/a	n/a
17	CTCF	chr6:29648260-29648410	GM12873	blood:	n/a	chr6:29648349-29648358
18	TAF1	chr6:29648154-29648378	GM12891	blood:	n/a	n/a
19	CTCF	chr6:29648270-29648444	H1-hESC	embryonic stem cell:	n/a	chr6:29648349-29648358
20	CTCF	chr6:29648237-29648432	GM12891	blood:	n/a	chr6:29648349-29648358
21	CTCF	chr6:29648260-29648410	HEK293	kidney:	n/a	chr6:29648349-29648358
22	CTCF	chr6:29648176-29648470	H1-hESC	embryonic stem cell:	n/a	chr6:29648349-29648358
23	CTCF	chr6:29648306-29648401	MCF-7	breast:	n/a	chr6:29648349-29648358
24	CTCF	chr6:29648320-29648470	HEK293	kidney:	n/a	chr6:29648349-29648358
25	POLR2A	chr6:29648091-29648540	GM12891	blood:	n/a	n/a
26	CTCF	chr6:29648260-29648410	GM12868	blood:	n/a	chr6:29648349-29648358
27	CTCF	chr6:29648320-29648470	GM12875	blood:	n/a	chr6:29648349-29648358
28	CTCF	chr6:29648320-29648470	HepG2	liver:	n/a	chr6:29648349-29648358

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29648348-29648398	MCF-7	breast:	n/a
2	chr6:29648360-29648410	SAEC	small airway:	n/a
3	chr6:29648348-29648398	AG04450	lung:	fetal
4	chr6:29648360-29648410	HL-60	blood:	n/a
5	chr6:29648360-29648410	HEEpiC	esophagus:	n/a
6	chr6:29648360-29648410	GM19239	blood:	n/a
7	chr6:29648360-29648410	NHDF-neo	bronchial:	n/a
8	chr6:29648360-29648410	Hepatocyte	liver:	n/a
9	chr6:29648348-29648398	HPAEpiC	pulmonary alveolar:	n/a
10	chr6:29648360-29648410	HCT-116	colon:	n/a
11	chr6:29648345-29648395	MCF-7	breast:	n/a
12	chr6:29648345-29648395	GM12891	blood:	n/a
13	chr6:29648360-29648410	HEK293	kidney:	embryo
14	chr6:29648360-29648410	HUVEC	blood vessel:	n/a
15	chr6:29648348-29648398	HAEpiC	amniotic membrane:	n/a
16	chr6:29648345-29648395	RPTEC	kidney:	n/a
17	chr6:29648345-29648395	PrEC	prostate:	n/a
18	chr6:29648348-29648398	HL-60	blood:	n/a
19	chr6:29648348-29648398	SKMC	muscle:	n/a
20	chr6:29648360-29648410	HRE	kidney:	n/a
21	chr6:29648360-29648410	H1-hESC	embryonic stem cell:	embryo
22	chr6:29648360-29648410	BJ	skin:	n/a
23	chr6:29648360-29648410	Hela-S3	cervix:	n/a
24	chr6:29648348-29648398	HUVEC	blood vessel:	n/a
25	chr6:29648345-29648395	NH-A	brain:	n/a
26	chr6:29648360-29648410	T-47D	breast:	n/a
27	chr6:29648360-29648410	NH-A	brain:	n/a
28	chr6:29648345-29648395	MCF10A-Er-Src	breast:	n/a
29	chr6:29648345-29648395	Hela-S3	cervix:	n/a
30	chr6:29648348-29648398	NB4	blood:	n/a
31	chr6:29648360-29648410	HRPEpiC	eye:	n/a
32	chr6:29648345-29648395	AoSMC	blood vessel:	n/a
33	chr6:29648360-29648410	A549	lung:	n/a
34	chr6:29648348-29648398	GM19239	blood:	n/a
35	chr6:29648348-29648398	H1-hESC	embryonic stem cell:	embryo
36	chr6:29648348-29648398	HEK293	kidney:	embryo
37	chr6:29648345-29648395	HAEpiC	amniotic membrane:	n/a
38	chr6:29648345-29648395	AG09309	skin:	n/a
39	chr6:29648348-29648398	CMK	blood:	n/a
40	chr6:29648360-29648410	GM12878	blood:	n/a
41	chr6:29648348-29648398	HCT-116	colon:	n/a
42	chr6:29648345-29648395	HEEpiC	esophagus:	n/a
43	chr6:29648348-29648398	ECC-1	luminal epithelium:	n/a
44	chr6:29648348-29648398	HNPCEpiC	eye:	n/a
45	chr6:29648348-29648398	AG04449	skin:	fetal
46	chr6:29648348-29648398	AG09319	gingival:	n/a
47	chr6:29648348-29648398	HCF	heart:	n/a
48	chr6:29648345-29648395	GM12878	blood:	n/a
49	chr6:29648348-29648398	HepG2	liver:	n/a
50	chr6:29648345-29648395	Caco-2	colon:	n/a

Variant related genes	Relation type
ZFP57	TF binding region
ZFP57	CpG island

Extended variants
information (count: 107 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1632956	0.95[YRI][hapmap]
rs2107203	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2158290	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2535238	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535240	0.85[EUR][1000 genomes]
rs2535274	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2535275	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747421	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747428	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747430	0.83[AFR][1000 genomes]
rs2747431	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2747457	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2747460	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747467	0.81[AFR][1000 genomes]
rs2907897	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29218	0.92[ASN][1000 genomes]
rs29228	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094579	0.98[ASN][1000 genomes]
rs3094724	0.83[ASN][1000 genomes]
rs3094725	0.84[ASN][1000 genomes]
rs3094730	0.81[ASN][1000 genomes]
rs3094731	0.81[ASN][1000 genomes]
rs3094732	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3094734	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3095266	0.84[ASN][1000 genomes]
rs3095269	0.92[ASN][1000 genomes]
rs3095271	0.93[ASN][1000 genomes]
rs3095284	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095290	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3095294	0.88[ASN][1000 genomes]
rs3116802	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3116803	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3116804	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3116811	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3116814	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3117289	0.93[ASN][1000 genomes]
rs3117295	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3117299	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3117301	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3117312	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3117318	0.93[ASN][1000 genomes]
rs3129033	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129035	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129039	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129042	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3129046	0.81[ASN][1000 genomes]
rs3129047	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129048	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129055	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129056	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129058	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129061	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129062	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129063	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129065	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129066	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129067	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3129069	0.93[ASN][1000 genomes]
rs3129070	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129072	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129073	0.93[ASN][1000 genomes]
rs3129084	0.85[ASN][1000 genomes]
rs3129086	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129092	0.85[ASN][1000 genomes]
rs3130251	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131865	0.82[ASN][1000 genomes]
rs3131866	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131867	0.81[ASN][1000 genomes]
rs3131868	0.82[ASN][1000 genomes]
rs3131870	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131871	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131872	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131873	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131874	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131884	0.80[ASN][1000 genomes]
rs3131889	0.80[ASN][1000 genomes]
rs3131890	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131895	0.86[ASN][1000 genomes]
rs3131898	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs365052	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs374317	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375248	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375984	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376319	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387640	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387642	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396660	0.83[AFR][1000 genomes]
rs416568	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs417764	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445150	0.83[AFR][1000 genomes]
rs448380	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448489	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258017	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9258048	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9258068	0.80[ASN][1000 genomes]
rs9258074	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9258078	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9258079	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258083	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9258087	0.80[EUR][1000 genomes]
rs9258088	0.80[EUR][1000 genomes]
rs9258104	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv10808	chr6:29648051-29653183	Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2747429	HLA-K	cis	lung	GTEx
rs2747429	ZFP57	cis	Whole Blood	GTEx
rs2747429	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2747429	ZNF323	cis	parietal	SCAN
rs2747429	ZFP57	cis	Artery Aorta	GTEx
rs2747429	ZFP57	cis	lymphoblastoid	seeQTL
rs2747429	ZNRD1	cis	lymphoblastoid	seeQTL
rs2747429	ZFP57	cis	Esophagus Mucosa	GTEx
rs2747429	ZFP57	cis	Esophagus Muscularis	GTEx
rs2747429	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs2747429	HIST1H2BM	cis	cerebellum	SCAN
rs2747429	HLA-F-AS1	cis	Whole Blood	GTEx
rs2747429	HLA-K	cis	Whole Blood	GTEx
rs2747429	ZFP57	cis	Heart Left Ventricle	GTEx
rs2747429	ZFP57	cis	Stomach	GTEx
rs2747429	ZFP57	cis	lung	GTEx
rs2747429	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2747429	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2747429	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx
rs2747429	ZFP57	cis	Adipose Subcutaneous	GTEx
rs2747429	ZFP57	cis	Thyroid	GTEx
rs2747429	ZFP57	cis	Artery Tibial	GTEx
rs2747429	HLA-A	cis	lymphoblastoid	GTEx
rs2747429	ZFP57	cis	Nerve Tibial	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29643000-29648800	Enhancers	HMEC	breast
3	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:29645200-29648400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:29646000-29648400	Flanking Active TSS	NHEK	skin
7	chr6:29646000-29648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:29646000-29651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:29646200-29651400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:29646200-29651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:29646400-29648400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:29646800-29651400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:29647000-29649600	Weak transcription	Spleen	Spleen
14	chr6:29647000-29651400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:29647000-29651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:29647400-29651600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:29647600-29649200	Active TSS	Fetal Heart	heart
18	chr6:29647800-29648800	Flanking Bivalent TSS/Enh	Placenta	Placenta
19	chr6:29647800-29649000	Bivalent/Poised TSS	Colonic Mucosa	Colon
20	chr6:29648000-29648600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:29648000-29648800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:29648000-29648800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:29648000-29649200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr6:29648000-29649200	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
25	chr6:29648000-29651400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:29648200-29648400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:29648200-29648400	Bivalent/Poised TSS	Primary B cells from peripheral blood	blood
28	chr6:29648200-29648600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:29648200-29648600	Flanking Bivalent TSS/Enh	K562	blood
30	chr6:29648200-29648600	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
31	chr6:29648200-29648800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr6:29648200-29649000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:29648200-29649000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr6:29648200-29649000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:29648200-29649000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:29648200-29649200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
37	chr6:29648200-29651400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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