Variant report

Variant	rs12656199
Chromosome Location	chr5:43495777-43495778
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	HEY1	chr5:43495152-43496644	K562	blood:	n/a	n/a
2	ZBTB33	chr5:43494898-43496735	K562	blood:	n/a	n/a
3	IRF4	chr5:43495432-43495896	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:43494914-43496199	GM12878	blood:	n/a	n/a
5	HEY1	chr5:43495468-43495802	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:43495103-43496065	GM12891	blood:	n/a	n/a
7	POLR2A	chr5:43495119-43496589	H1-hESC	embryonic stem cell:	n/a	n/a
8	HEY1	chr5:43495432-43495862	K562	blood:	n/a	n/a
9	POLR2A	chr5:43494763-43496825	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:43495495-43495824	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:43494936-43496658	GM12892	blood:	n/a	n/a
12	POU2F2	chr5:43495349-43495895	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:43495490-43495880	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:43495389-43495954	GM12891	blood:	n/a	n/a
15	GATA2	chr5:43495468-43495817	K562	blood:	n/a	n/a
16	POLR2A	chr5:43495174-43496206	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:43495040-43496668	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:43495036-43496635	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:43495158-43496627	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:43495233-43496683	GM12892	blood:	n/a	n/a
21	POLR2A	chr5:43495517-43496008	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:43495505-43495956	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:43495418-43496629	GM12891	blood:	n/a	n/a
24	POLR2A	chr5:43495094-43496668	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
C5orf34	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10461740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10941642	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12653472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653645	0.81[ASN][1000 genomes]
rs12656650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658205	1.00[AMR][1000 genomes]
rs12659627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13158442	1.00[AMR][1000 genomes]
rs13161668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161770	1.00[AMR][1000 genomes]
rs13165869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167838	1.00[AMR][1000 genomes]
rs13168053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183746	0.93[ASN][1000 genomes]
rs13188884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34141186	0.81[ASN][1000 genomes]
rs34179982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34211578	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34350522	1.00[AMR][1000 genomes]
rs34455365	1.00[AMR][1000 genomes]
rs34512505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34617389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34788563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792822	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34868623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34973456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34980504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34991197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136550	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35171369	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35478855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590922	1.00[AMR][1000 genomes]
rs35602154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35707409	1.00[AMR][1000 genomes]
rs35713376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35733458	1.00[AMR][1000 genomes]
rs35923573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35966682	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs36076336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36104847	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4533897	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs71629170	1.00[AMR][1000 genomes]
rs71629171	1.00[AMR][1000 genomes]
rs71629172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71629174	1.00[AMR][1000 genomes]
rs71629175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71629177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71629178	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71629180	1.00[AMR][1000 genomes];0.81[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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	220 gene(s)	inside rSNPs	diseases
3	nsv964848	chr5:43495039-43497079	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43484800-43498000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:43484800-43502800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:43484800-43502800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:43484800-43502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:43484800-43502800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:43484800-43505600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:43484800-43511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:43484800-43514000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:43484800-43514600	Weak transcription	Ovary	ovary
10	chr5:43484800-43514800	Weak transcription	Spleen	Spleen
11	chr5:43485000-43497800	Weak transcription	Placenta	Placenta
12	chr5:43485000-43501000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:43485000-43501000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:43485000-43502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:43485000-43503000	Weak transcription	NHEK	skin
16	chr5:43485000-43503400	Weak transcription	Brain Germinal Matrix	brain
17	chr5:43485000-43504600	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:43485000-43505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:43485000-43513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:43485000-43513800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:43485000-43514200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:43485200-43502800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:43485200-43505400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:43485200-43505400	Weak transcription	Fetal Intestine Large	intestine
25	chr5:43485200-43505400	Weak transcription	Fetal Stomach	stomach
26	chr5:43485200-43506000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:43485200-43506000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:43485200-43513200	Weak transcription	NHDF-Ad	bronchial
29	chr5:43485200-43513200	Weak transcription	NHLF	lung
30	chr5:43485200-43513400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:43485200-43513400	Weak transcription	Fetal Lung	lung
32	chr5:43485200-43513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:43485200-43513600	Weak transcription	Fetal Intestine Small	intestine
34	chr5:43485200-43513600	Weak transcription	HSMM	muscle
35	chr5:43485200-43513600	Weak transcription	NH-A	brain
36	chr5:43485200-43514200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:43485400-43495800	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:43485400-43501200	Weak transcription	A549	lung
39	chr5:43485400-43502800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:43485400-43505400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:43485400-43514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:43485800-43503000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:43485800-43505200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:43485800-43505600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:43485800-43514200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:43486000-43497600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr5:43486000-43501200	Weak transcription	Osteobl	bone
48	chr5:43486000-43503000	Weak transcription	Thymus	Thymus
49	chr5:43486000-43509800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:43486000-43514200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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