Variant report

Variant	rs2529
Chromosome Location	chr7:64147169-64147170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr7:64147128-64147276	GM12878	blood:	n/a	n/a
2	ELF1	chr7:64146880-64147200	HepG2	liver:	n/a	n/a
3	RUNX3	chr7:64146830-64147298	GM12878	blood:	n/a	n/a
4	ELF1	chr7:64146848-64147390	MCF-7	breast:	n/a	n/a
5	SPI1	chr7:64146822-64147321	HL-60	blood:	n/a	n/a
6	EP300	chr7:64146876-64147338	HepG2	liver:	n/a	n/a
7	STAT5A	chr7:64146726-64147355	GM12878	blood:	n/a	n/a
8	ESR1	chr7:64146826-64147193	T-47D	breast:	n/a	n/a
9	EP300	chr7:64146808-64147340	T-47D	breast:	n/a	n/a
10	FOXA2	chr7:64146880-64147562	HepG2	liver:	n/a	n/a
11	YY1	chr7:64146788-64147286	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:64146849-64147429	HL-60	blood:	n/a	n/a
13	POLR2A	chr7:64147065-64147365	GM12891	blood:	n/a	n/a
14	EP300	chr7:64146835-64147380	HepG2	liver:	n/a	n/a
15	ATF2	chr7:64146982-64147307	GM12878	blood:	n/a	n/a
16	HDAC2	chr7:64146785-64147365	MCF-7	breast:	n/a	n/a
17	ESR1	chr7:64146876-64147229	T-47D	breast:	n/a	n/a
18	MAX	chr7:64146756-64147419	MCF-7	breast:	n/a	n/a
19	ELF1	chr7:64146829-64147269	GM12878	blood:	n/a	n/a
20	NFATC1	chr7:64146934-64147345	GM12878	blood:	n/a	n/a
21	MYBL2	chr7:64146902-64147412	HepG2	liver:	n/a	n/a
22	SP1	chr7:64146863-64147398	HepG2	liver:	n/a	n/a
23	CEBPB	chr7:64146864-64147335	MCF-7	breast:	n/a	n/a
24	NFATC1	chr7:64146909-64147375	GM12878	blood:	n/a	n/a
25	RUNX3	chr7:64146779-64147371	GM12878	blood:	n/a	n/a
26	FOXA1	chr7:64146860-64147310	T-47D	breast:	n/a	chr7:64147116-64147131
27	MAX	chr7:64147036-64147243	NB4	blood:	n/a	n/a
28	MTA3	chr7:64146762-64147407	GM12878	blood:	n/a	n/a
29	NFIC	chr7:64146907-64147425	GM12878	blood:	n/a	n/a
30	MAX	chr7:64146808-64147455	HepG2	liver:	n/a	n/a
31	ARID3A	chr7:64146938-64147288	HepG2	liver:	n/a	n/a
32	POLR2A	chr7:64144467-64147798	GM12891	blood:	n/a	n/a
33	GATA3	chr7:64146829-64147374	MCF-7	breast:	n/a	n/a
34	CEBPB	chr7:64146821-64147409	MCF-7	breast:	n/a	n/a
35	FOXA1	chr7:64146818-64147332	HepG2	liver:	n/a	chr7:64147116-64147131
36	CEBPB	chr7:64146943-64147249	HepG2	liver:	n/a	n/a
37	ESR1	chr7:64146840-64147221	T-47D	breast:	n/a	n/a
38	CEBPB	chr7:64146948-64147216	HepG2	liver:	n/a	n/a
39	POLR2A	chr7:64146604-64147523	HL-60	blood:	n/a	n/a
40	HA-E2F1	chr7:64146877-64147428	MCF-7	breast:	n/a	n/a
41	FOXA2	chr7:64146810-64147304	HepG2	liver:	n/a	n/a
42	FOXA1	chr7:64146863-64147329	HepG2	liver:	n/a	chr7:64147116-64147131
43	EP300	chr7:64146917-64147227	HepG2	liver:	n/a	n/a
44	NR2F2	chr7:64146818-64147418	MCF-7	breast:	n/a	n/a
45	FOXA1	chr7:64146861-64147339	T-47D	breast:	n/a	chr7:64147116-64147131
46	BCLAF1	chr7:64146861-64147273	GM12878	blood:	n/a	n/a
47	EP300	chr7:64146697-64147287	T-47D	breast:	n/a	n/a
48	POLR2A	chr7:64146927-64147532	GM12878	blood:	n/a	n/a
49	ELF1	chr7:64146721-64147361	MCF-7	breast:	n/a	n/a
50	FOXA1	chr7:64146840-64147336	HepG2	liver:	n/a	chr7:64147116-64147131

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:64138840..64143249-chr7:64144344..64147303,3	K562	blood:
2	chr7:64125080..64128959-chr7:64143328..64147169,6	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-3	chr7:64144713-64147263	NONHSAT121038
2	lnc-ZNF138-3	chr7:64144713-64148208	NR_104148
3	lnc-ZNF138-3	chr7:64144713-64148208	NR_104149

No data

Variant related genes	Relation type
ZNF107	TF binding region
ENSG00000196247	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1104867	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768255	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230561	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13231070	0.94[ASN][1000 genomes]
rs1596929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17779754	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838901	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2862793	0.81[CEU][hapmap]
rs2862797	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2862798	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2902328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126100	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718100	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718102	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718103	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460173	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651043	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651044	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962303	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73361894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7385908	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
4	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031703	chr7:63839601-64225952	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
11	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1021893	chr7:63995601-64155027	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv538892	chr7:63995601-64155027	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
15	esv16290	chr7:64058602-64162829	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
16	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
17	nsv970856	chr7:64126256-64155821	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2529	ZNF588	cis	normal skin	skin_eQTL
rs2529	ZNF107	cis	Muscle Skeletal	GTEx
rs2529	ZNF107	cis	parietal	SCAN
rs2529	ZNF107	cis	Esophagus Muscularis	GTEx
rs2529	ZNF107	cis	Stomach	GTEx
rs2529	LOC168474	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64127400-64153600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:64128200-64167600	Weak transcription	Hela-S3	cervix
3	chr7:64128200-64168000	Weak transcription	Brain Angular Gyrus	brain
4	chr7:64128800-64168000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:64138400-64152600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr7:64138600-64147400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr7:64138600-64153000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr7:64138600-64162200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:64138600-64168400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:64138800-64147800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr7:64138800-64153000	ZNF genes & repeats	GM12878-XiMat	blood
12	chr7:64139000-64149000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:64139200-64147400	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr7:64139400-64147400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr7:64139400-64147400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr7:64139400-64148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:64139400-64148000	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr7:64139400-64148000	ZNF genes & repeats	Thymus	Thymus
19	chr7:64139400-64148600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:64139400-64148600	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr7:64139400-64153000	ZNF genes & repeats	Fetal Brain Female	brain
22	chr7:64139400-64155000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr7:64139600-64147400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr7:64139600-64148000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:64139600-64148000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:64139600-64149000	ZNF genes & repeats	Fetal Thymus	thymus
27	chr7:64139800-64148000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
28	chr7:64140200-64147600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:64140800-64147400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:64140800-64148000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr7:64140800-64148600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:64141000-64148000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:64141000-64159800	Weak transcription	Stomach Mucosa	stomach
34	chr7:64141200-64147200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:64141200-64148000	ZNF genes & repeats	Spleen	Spleen
36	chr7:64141400-64147800	Strong transcription	K562	blood
37	chr7:64141400-64148000	Strong transcription	Pancreas	Pancrea
38	chr7:64141400-64149600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:64141800-64147400	Strong transcription	HSMMtube	muscle
40	chr7:64142200-64147600	Strong transcription	Adipose Nuclei	Adipose
41	chr7:64142800-64149000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr7:64143200-64147800	ZNF genes & repeats	Liver	Liver
43	chr7:64143200-64148000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:64143200-64148200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:64143200-64148600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr7:64143600-64147400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:64143600-64148600	Strong transcription	Left Ventricle	heart
48	chr7:64143800-64167000	Weak transcription	Fetal Heart	heart
49	chr7:64144000-64147200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:64144400-64147400	ZNF genes & repeats	Fetal Lung	lung

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