Variant report

Variant	rs12475209
Chromosome Location	chr2:39742085-39742086
allele	G/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	TEAD4	chr2:39741859-39744517	HepG2	liver:	n/a	n/a
2	JUND	chr2:39742043-39742346	HepG2	liver:	n/a	chr2:39742191-39742202
3	NFIC	chr2:39741998-39745286	HepG2	liver:	n/a	n/a
4	FOXA2	chr2:39741986-39744260	HepG2	liver:	n/a	n/a
5	MYBL2	chr2:39741995-39744529	HepG2	liver:	n/a	n/a
6	RAD21	chr2:39740568-39742169	SK-N-SH	brain:	n/a	chr2:39740968-39740987

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39662739..39665168-chr2:39741315..39743608,2	K562	blood:
2	chr2:39741394..39743199-chr2:39794476..39796005,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39741287-39742486	ENSG00000231312.2

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10180761	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11900495	1.00[ASN][1000 genomes]
rs12476783	1.00[ASN][1000 genomes]
rs12993058	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1526025	1.00[ASN][1000 genomes]
rs17467001	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17473802	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35368235	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
2	chr2:39724800-39750600	Weak transcription	Gastric	stomach
3	chr2:39733000-39743600	Weak transcription	Hela-S3	cervix
4	chr2:39734600-39745000	Enhancers	Adipose Nuclei	Adipose
5	chr2:39734600-39746000	Enhancers	Fetal Heart	heart
6	chr2:39735000-39744800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:39736400-39745000	Enhancers	Right Atrium	heart
8	chr2:39736400-39745000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:39737000-39744800	Enhancers	Fetal Muscle Leg	muscle
10	chr2:39737000-39745000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:39737400-39743000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:39738000-39745000	Enhancers	Duodenum Mucosa	Duodenum
13	chr2:39738800-39743000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39738800-39743000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:39739400-39743600	Enhancers	HUVEC	blood vessel
16	chr2:39739600-39742600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:39739600-39742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:39739600-39743200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:39739800-39742600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:39739800-39742600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:39739800-39743400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:39739800-39744200	Enhancers	K562	blood
23	chr2:39739800-39745600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:39740200-39743600	Weak transcription	Fetal Brain Male	brain
25	chr2:39740400-39742400	Weak transcription	Fetal Intestine Large	intestine
26	chr2:39740600-39745000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr2:39740800-39742200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:39740800-39742600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:39740800-39742800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:39740800-39743400	Enhancers	Lung	lung
31	chr2:39740800-39745000	Enhancers	Left Ventricle	heart
32	chr2:39741000-39742600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:39741200-39742400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:39741200-39742600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:39741200-39742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:39741200-39743400	Weak transcription	Small Intestine	intestine
37	chr2:39741200-39743800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:39741400-39742400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:39741400-39742400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:39741400-39742400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:39741400-39742400	Weak transcription	Fetal Stomach	stomach
42	chr2:39741400-39742600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:39741400-39742600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:39741400-39742600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:39741400-39742600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:39741400-39742600	Weak transcription	Brain Angular Gyrus	brain
47	chr2:39741400-39742600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:39741400-39742600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:39741400-39742600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:39741400-39742800	Weak transcription	Colon Smooth Muscle	Colon

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