Variant report

Variant	rs2790052
Chromosome Location	chr1:165738463-165738464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:415)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:415 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELK1	chr1:165737720-165738839	GM12878	blood:	n/a	n/a
2	MYC	chr1:165737582-165738944	K562	blood:	n/a	n/a
3	SIN3AK20	chr1:165737596-165738670	K562	blood:	n/a	n/a
4	ZBTB33	chr1:165737953-165738494	GM12878	blood:	n/a	chr1:165738241-165738256
5	FOSL2	chr1:165737907-165738679	HepG2	liver:	n/a	chr1:165738669-165738678
6	ZBTB33	chr1:165737937-165738480	HepG2	liver:	n/a	chr1:165738241-165738256
7	MAZ	chr1:165737623-165738678	Hela-S3	cervix:	n/a	n/a
8	ZBTB33	chr1:165737940-165738517	K562	blood:	n/a	chr1:165738241-165738256
9	ZMIZ1	chr1:165737377-165739133	K562	blood:	n/a	n/a
10	CCNT2	chr1:165738045-165738526	K562	blood:	n/a	n/a
11	RCOR1	chr1:165737636-165738954	K562	blood:	n/a	n/a
12	TRIM28	chr1:165737501-165738789	K562	blood:	n/a	n/a
13	KAP1	chr1:165737845-165738535	U2OS	brain:	n/a	n/a
14	YY1	chr1:165737863-165738625	GM12892	blood:	n/a	n/a
15	ZBTB33	chr1:165737748-165738813	SK-N-SH	brain:	n/a	chr1:165738241-165738256
16	POLR2A	chr1:165737852-165738650	HepG2	liver:	n/a	n/a
17	ELF1	chr1:165737880-165738567	A549	lung:	n/a	n/a
18	GTF2F1	chr1:165737912-165738566	H1-hESC	embryonic stem cell:	n/a	n/a
19	ELF1	chr1:165737721-165738648	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:165737830-165738686	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr1:165737920-165738735	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr1:165737753-165738807	A549	lung:	n/a	n/a
23	TCF12	chr1:165737708-165738752	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr1:165737551-165739622	HepG2	liver:	n/a	n/a
25	RUNX3	chr1:165737830-165738798	GM12878	blood:	n/a	n/a
26	REST	chr1:165737758-165738924	HL-60	blood:	n/a	n/a
27	POLR2A	chr1:165737816-165738653	H1-hESC	embryonic stem cell:	n/a	n/a
28	RCOR1	chr1:165737674-165738769	K562	blood:	n/a	n/a
29	SIX5	chr1:165737726-165738752	A549	lung:	n/a	n/a
30	SP1	chr1:165737866-165738549	A549	lung:	n/a	n/a
31	ZBTB33	chr1:165737889-165738485	HCT-116	colon:	n/a	chr1:165738241-165738256
32	POLR2A	chr1:165737827-165738601	A549	lung:	n/a	n/a
33	NR2F2	chr1:165737731-165738917	K562	blood:	n/a	n/a
34	GABPA	chr1:165737575-165738780	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:165737646-165739273	GM18505	blood:	n/a	n/a
36	SPI1	chr1:165737827-165738819	HL-60	blood:	n/a	n/a
37	POLR2A	chr1:165737828-165738705	GM12891	blood:	n/a	n/a
38	MAFF	chr1:165737945-165739075	K562	blood:	n/a	n/a
39	STAT5A	chr1:165737786-165738744	K562	blood:	n/a	n/a
40	POLR2A	chr1:165737685-165738956	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr1:165737673-165738748	K562	blood:	n/a	n/a
42	YY1	chr1:165737831-165738665	GM12878	blood:	n/a	n/a
43	MAX	chr1:165737703-165738743	HCT-116	colon:	n/a	n/a
44	ELF1	chr1:165737865-165738635	K562	blood:	n/a	n/a
45	POLR2A	chr1:165737524-165739409	GM12878	blood:	n/a	n/a
46	MAX	chr1:165737662-165738717	K562	blood:	n/a	n/a
47	HEY1	chr1:165737636-165738781	K562	blood:	n/a	n/a
48	TCF12	chr1:165737876-165738667	ECC-1	luminal epithelium:	n/a	n/a
49	FOSL2	chr1:165737902-165738791	A549	lung:	n/a	chr1:165738669-165738678
50	CEBPB	chr1:165737731-165738676	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
2	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:
3	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
4	chr1:165601421..165603432-chr1:165737509..165739117,2	K562	blood:
5	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
6	chr1:165599820..165600395-chr1:165738023..165738865,2	Hela-S3	cervix:
7	chr1:165737902..165738807-chr17:56736250..56737011,2	MCF-7	breast:
8	chr1:165737601..165739848-chr12:7052889..7054535,2	MCF-7	breast:
9	chr1:165738046..165738606-chr19:12903390..12903916,2	Hela-S3	cervix:
10	chr1:165667536..165669486-chr1:165736821..165739691,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UCK2-1	chr1:165738166-165738612	ENSG00000224358
2	lnc-UCK2-1	chr1:165738166-165738612	NONHSAT007334

No data

Variant related genes	Relation type
TMCO1	TF binding region
ENSG00000238923	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000215838	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2790049	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][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]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.80[EUR][1000 genomes]
rs4233408	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165737000-165739200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:165737000-165739400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:165737200-165738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:165737200-165739000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:165737200-165739000	Active TSS	Fetal Intestine Large	intestine
6	chr1:165737200-165739000	Active TSS	Lung	lung
7	chr1:165737200-165739000	Active TSS	Psoas Muscle	Psoas
8	chr1:165737200-165739200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:165737200-165739200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:165737200-165739200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:165737200-165739200	Active TSS	Right Atrium	heart
12	chr1:165737200-165739400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:165737200-165739400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:165737200-165739600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:165737400-165738600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:165737400-165738600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:165737400-165738600	Active TSS	Fetal Muscle Leg	muscle
18	chr1:165737400-165738600	Active TSS	Placenta	Placenta
19	chr1:165737400-165738800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:165737400-165738800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:165737400-165738800	Active TSS	Brain Germinal Matrix	brain
22	chr1:165737400-165738800	Active TSS	Fetal Intestine Small	intestine
23	chr1:165737400-165738800	Active TSS	Fetal Stomach	stomach
24	chr1:165737400-165739000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:165737400-165739000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:165737400-165739000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:165737400-165739000	Active TSS	Primary T cells fromperipheralblood	blood
28	chr1:165737400-165739000	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:165737400-165739000	Active TSS	Aorta	Aorta
30	chr1:165737400-165739000	Active TSS	Left Ventricle	heart
31	chr1:165737400-165739000	Active TSS	Ovary	ovary
32	chr1:165737400-165739000	Active TSS	Placenta Amnion	Placenta Amnion
33	chr1:165737400-165739000	Bivalent/Poised TSS	HepG2	liver
34	chr1:165737400-165739200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:165737400-165739200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:165737400-165739200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:165737400-165739200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:165737400-165739200	Active TSS	Colonic Mucosa	Colon
39	chr1:165737400-165739200	Active TSS	Fetal Muscle Trunk	muscle
40	chr1:165737400-165739200	Active TSS	Right Ventricle	heart
41	chr1:165737400-165739400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:165737400-165739400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:165737400-165739400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:165737400-165739400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:165737400-165739400	Active TSS	A549	lung
46	chr1:165737400-165740200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:165737600-165738600	Active TSS	Brain Substantia Nigra	brain
48	chr1:165737600-165738600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr1:165737600-165738600	Active TSS	Fetal Brain Male	brain
50	chr1:165737600-165738600	Active TSS	Fetal Heart	heart

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