Variant report

Variant	rs13005601
Chromosome Location	chr2:179388657-179388658
allele	A/G
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	RCOR1	chr2:179388558-179388759	GM12878	blood:	n/a	n/a
2	MYC	chr2:179387456-179388704	K562	blood:	n/a	chr2:179387821-179387830
3	POLR2A	chr2:179387582-179388811	GM19099	blood:	n/a	n/a
4	MAZ	chr2:179387317-179388681	IMR90	lung:	n/a	chr2:179387821-179387830
5	MXI1	chr2:179387490-179388775	IMR90	lung:	n/a	n/a
6	MXI1	chr2:179388428-179388740	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:179387612-179388695	K562	blood:	n/a	n/a
8	MTA3	chr2:179387464-179388665	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:179387596-179388764	K562	blood:	n/a	n/a
10	MAFK	chr2:179387381-179388737	K562	blood:	n/a	chr2:179387865-179387876 chr2:179387865-179387876 chr2:179387865-179387880 chr2:179387866-179387877
11	TEAD4	chr2:179387586-179388865	K562	blood:	n/a	n/a
12	SIN3A	chr2:179388651-179388719	H1-hESC	embryonic stem cell:	n/a	n/a
13	MXI1	chr2:179387231-179389438	SK-N-SH	brain:	n/a	n/a
14	HCFC1	chr2:179387539-179388785	K562	blood:	n/a	n/a
15	POLR2A	chr2:179387637-179388821	GM12892	blood:	n/a	n/a
16	POLR2A	chr2:179387714-179388726	Raji	blood:	n/a	n/a
17	BHLHE40	chr2:179388430-179388672	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:179387555-179388923	GM12891	blood:	n/a	n/a
19	WRNIP1	chr2:179387608-179388729	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:179387644-179388681	PBDE	blood:	n/a	n/a
21	CHD1	chr2:179387119-179388906	IMR90	lung:	n/a	n/a
22	POLR2A	chr2:179388300-179388734	GM12891	blood:	n/a	n/a
23	NR2F2	chr2:179387426-179388849	K562	blood:	n/a	n/a
24	YY1	chr2:179388492-179388706	K562	blood:	n/a	n/a
25	MAX	chr2:179388503-179388774	K562	blood:	n/a	n/a
26	POLR2A	chr2:179387609-179388804	GM12878	blood:	n/a	n/a
27	MYC	chr2:179387538-179388761	NB4	blood:	n/a	chr2:179387821-179387830
28	ZNF263	chr2:179387624-179388857	HEK293-T-REx	kidney:	n/a	chr2:179387956-179387977

No.	Distal block	Cell Line	Cell type
1	chr2:179314051..179317404-chr2:179386204..179389847,5	K562	blood:
2	chr2:179386627..179389310-chr2:179394176..179396606,2	MCF-7	breast:
3	chr2:179343391..179346043-chr2:179387218..179389955,4	K562	blood:
4	chr2:179386919..179391089-chr2:179391647..179398872,11	K562	blood:
5	chr2:179315192..179318591-chr2:179386093..179388793,4	K562	blood:

Variant related genes	Relation type
TTN-AS1	TF binding region
ENSG00000204311	Chromatin interaction
ENSG00000237298	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1007025	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12614435	0.81[CEU][hapmap]
rs12618265	0.90[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12998857	0.81[CEU][hapmap]
rs13009158	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13029629	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13034990	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16866358	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16866365	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16866369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866373	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16866397	0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16866406	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288325	0.90[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288569	1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288571	0.82[CEU][hapmap]
rs2303539	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857265	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731748	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731749	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731751	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829747	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829748	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755456	0.82[CEU][hapmap]
rs744426	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7597154	0.90[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890578	0.81[CEU][hapmap]

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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 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	chr2:179387200-179389400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr2:179387400-179388800	Active TSS	Fetal Intestine Large	intestine
3	chr2:179387400-179388800	Active TSS	Fetal Intestine Small	intestine
4	chr2:179387400-179389000	Active TSS	Brain Angular Gyrus	brain
5	chr2:179387400-179389000	Active TSS	Brain Hippocampus Middle	brain
6	chr2:179387400-179389000	Active TSS	Fetal Stomach	stomach
7	chr2:179387400-179389200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:179387400-179389200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:179387400-179389200	Active TSS	Brain Anterior Caudate	brain
10	chr2:179387400-179389200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr2:179387400-179389200	Active TSS	Ovary	ovary
12	chr2:179387400-179389200	Active TSS	NHLF	lung
13	chr2:179387400-179389400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:179387400-179389400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:179387400-179389400	Active TSS	Brain Cingulate Gyrus	brain
16	chr2:179387400-179389400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:179387400-179389400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:179387400-179389400	Active TSS	HepG2	liver
19	chr2:179387400-179389600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:179387600-179388800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr2:179387600-179388800	Active TSS	Duodenum Mucosa	Duodenum
22	chr2:179387600-179388800	Active TSS	Esophagus	oesophagus
23	chr2:179387600-179388800	Active TSS	Fetal Kidney	kidney
24	chr2:179387600-179388800	Active TSS	Fetal Muscle Trunk	muscle
25	chr2:179387600-179388800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:179387600-179389000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:179387600-179389000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:179387600-179389000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:179387600-179389000	Active TSS	Aorta	Aorta
30	chr2:179387600-179389000	Active TSS	Fetal Brain Female	brain
31	chr2:179387600-179389000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:179387600-179389200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:179387600-179389200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:179387600-179389200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:179387600-179389200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr2:179387600-179389200	Active TSS	Rectal Smooth Muscle	rectum
37	chr2:179387600-179389200	Active TSS	NHDF-Ad	bronchial
38	chr2:179387600-179389400	Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:179387600-179389400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:179387600-179389400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:179387600-179389400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr2:179387600-179389400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:179387600-179389400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:179387600-179389400	Active TSS	Brain Germinal Matrix	brain
45	chr2:179387600-179389400	Active TSS	A549	lung
46	chr2:179387600-179389400	Active TSS	Hela-S3	cervix
47	chr2:179387600-179389400	Active TSS	HMEC	breast
48	chr2:179387800-179388800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr2:179387800-179388800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:179387800-179388800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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