Variant report

Variant	rs3790666
Chromosome Location	chr1:165870263-165870264
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	FOXA1	chr1:165869850-165870366	HepG2	liver:	n/a	chr1:165870128-165870140
2	MYC	chr1:165869869-165870443	HUVEC	blood vessel:	n/a	chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870298-165870307
3	MAX	chr1:165869366-165870499	HUVEC	blood vessel:	n/a	chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870298-165870307
4	POLR2A	chr1:165864447-165870499	IMR90	lung:	n/a	n/a
5	KAP1	chr1:165869501-165870796	HEK293	kidney:	n/a	n/a
6	MYC	chr1:165870124-165870444	HepG2	liver:	n/a	chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870298-165870307
7	EP300	chr1:165869845-165870414	HepG2	liver:	n/a	n/a
8	MAX	chr1:165869923-165870408	HepG2	liver:	n/a	chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870298-165870307
9	MYBL2	chr1:165869774-165870383	HepG2	liver:	n/a	n/a
10	NR2F2	chr1:165869809-165870523	HepG2	liver:	n/a	n/a
11	ARID3A	chr1:165869902-165870312	HepG2	liver:	n/a	n/a
12	REST	chr1:165870257-165870796	H1-neurons	neurons:	n/a	chr1:165870307-165870315
13	POLR2A	chr1:165869683-165870628	HUVEC	blood vessel:	n/a	n/a
14	FOXA1	chr1:165869854-165870327	HepG2	liver:	n/a	chr1:165870128-165870140
15	MYBL2	chr1:165869829-165870432	HepG2	liver:	n/a	n/a
16	MAX	chr1:165869763-165870594	HepG2	liver:	n/a	chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870297-165870307 chr1:165870298-165870307
17	GATA2	chr1:165869872-165870553	HUVEC	blood vessel:	n/a	chr1:165870172-165870183
18	FOXA1	chr1:165869907-165870391	HepG2	liver:	n/a	chr1:165870128-165870140
19	POLR2A	chr1:165869814-165870488	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:165870195-165870543	K562	blood:	n/a	n/a
21	POLR2A	chr1:165870020-165870795	K562	blood:	n/a	n/a
22	REST	chr1:165870039-165870930	H1-neurons	neurons:	n/a	chr1:165870307-165870315 chr1:165870818-165870826
23	TCF7L2	chr1:165869963-165870414	HepG2	liver:	n/a	n/a
24	BHLHE40	chr1:165869828-165870315	HepG2	liver:	n/a	n/a
25	CEBPB	chr1:165869842-165870289	HepG2	liver:	n/a	chr1:165870064-165870075
26	HDAC2	chr1:165869962-165870334	HepG2	liver:	n/a	chr1:165870171-165870185 chr1:165870172-165870186
27	MXI1	chr1:165869890-165870408	HepG2	liver:	n/a	chr1:165870297-165870306
28	POLR2A	chr1:165870225-165870803	H1-neurons	neurons:	n/a	n/a
29	FOXA2	chr1:165869845-165870271	HepG2	liver:	n/a	chr1:165870128-165870140
30	CHD1	chr1:165864264-165870908	IMR90	lung:	n/a	n/a
31	NFIC	chr1:165869968-165870315	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:165870006-165870457	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr1:165870185-165870360	HUVEC	blood vessel:	n/a	n/a
34	HDAC2	chr1:165869829-165870329	HepG2	liver:	n/a	chr1:165870171-165870185 chr1:165870172-165870186
35	MAX	chr1:165869724-165870547	HepG2	liver:	n/a	chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870297-165870307 chr1:165870297-165870308 chr1:165870296-165870309 chr1:165870298-165870307

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165864751..165867551-chr1:165869428..165872327,2	MCF-7	breast:

Variant related genes	Relation type
UCK2	TF binding region
ENSG00000236364	TF binding region
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1061771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061772	0.97[AFR][1000 genomes]
rs10918307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084653	0.89[AFR][1000 genomes]
rs12090859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663840	1.00[EUR][1000 genomes]
rs16852574	0.89[AFR][1000 genomes]
rs2153261	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2153262	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2185267	1.00[EUR][1000 genomes]
rs2275432	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2349109	1.00[ASN][1000 genomes]
rs3748701	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790656	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790657	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790662	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790663	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790664	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790667	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806331	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806332	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61057126	0.94[AFR][1000 genomes]
rs6666697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73031410	0.94[AFR][1000 genomes]
rs73031470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165854600-165883000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:165856600-165878800	Weak transcription	Small Intestine	intestine
3	chr1:165858200-165881200	Strong transcription	Dnd41	blood
4	chr1:165858400-165881000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:165858600-165872000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:165858600-165872600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:165859000-165881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:165859200-165870400	Strong transcription	Fetal Stomach	stomach
10	chr1:165859200-165871000	Strong transcription	Primary hematopoietic stem cells	blood
11	chr1:165859200-165871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:165859200-165878000	Strong transcription	Hela-S3	cervix
13	chr1:165859200-165880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:165859200-165881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:165859400-165871200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:165859600-165870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:165859800-165870600	Strong transcription	Fetal Brain Female	brain
23	chr1:165860000-165880200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:165860400-165870400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:165862000-165871800	Weak transcription	Brain Substantia Nigra	brain
26	chr1:165862400-165871800	Weak transcription	Brain Anterior Caudate	brain
27	chr1:165864200-165870800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr1:165864600-165872000	Weak transcription	Primary B cells from cord blood	blood
29	chr1:165865000-165870600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:165865000-165872600	Weak transcription	Adipose Nuclei	Adipose
31	chr1:165866000-165871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:165866400-165870400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:165866400-165875000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:165866600-165871400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:165866600-165871800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:165866800-165872000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:165866800-165872200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:165866800-165872200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:165867000-165871800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:165867000-165872800	Enhancers	HUVEC	blood vessel
41	chr1:165867200-165876800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:165867400-165871000	Genic enhancers	HSMM	muscle
43	chr1:165867400-165872400	Weak transcription	Colonic Mucosa	Colon
44	chr1:165867600-165870400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:165867800-165870600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr1:165867800-165870600	Enhancers	Esophagus	oesophagus
47	chr1:165867800-165870600	Enhancers	Pancreas	Pancrea
48	chr1:165867800-165871200	Enhancers	Stomach Mucosa	stomach
49	chr1:165867800-165876600	Weak transcription	Psoas Muscle	Psoas
50	chr1:165868000-165870600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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