Variant report

Variant	rs2230550
Chromosome Location	chr12:49722793-49722794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49722561-49722878	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:49722790-49722806	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:49722656-49727114	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:49722651-49723270	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49721324..49723403-chr12:50016643..50018647,2	MCF-7	breast:
2	chr12:49666758..49668347-chr12:49722296..49724734,2	K562	blood:
3	chr12:49721808..49725568-chr12:49752625..49757232,4	MCF-7	breast:
4	chr12:49690281..49692402-chr12:49721783..49724364,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258334	TF binding region
ENSG00000135406	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10875946	0.93[ASN][1000 genomes]
rs10875948	0.93[ASN][1000 genomes]
rs11168967	0.93[ASN][1000 genomes]
rs11168970	0.93[ASN][1000 genomes]
rs11168971	0.93[ASN][1000 genomes]
rs11168972	0.93[ASN][1000 genomes]
rs11835037	0.93[ASN][1000 genomes]
rs11837234	0.93[ASN][1000 genomes]
rs12301545	0.93[ASN][1000 genomes]
rs12304800	0.93[ASN][1000 genomes]
rs12313435	0.93[ASN][1000 genomes]
rs12315095	0.93[ASN][1000 genomes]
rs12315130	0.93[ASN][1000 genomes]
rs12317532	0.93[ASN][1000 genomes]
rs12318618	1.00[ASN][1000 genomes]
rs12322335	0.93[ASN][1000 genomes]
rs12322798	0.93[ASN][1000 genomes]
rs12581307	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12581343	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581428	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070761	0.93[ASN][1000 genomes]
rs2236746	0.93[ASN][1000 genomes]
rs28543370	0.93[ASN][1000 genomes]
rs28798494	0.93[ASN][1000 genomes]
rs28823960	0.93[ASN][1000 genomes]
rs28857010	0.93[ASN][1000 genomes]
rs34791911	0.93[ASN][1000 genomes]
rs3898446	0.93[ASN][1000 genomes]
rs4898516	0.93[ASN][1000 genomes]
rs4898517	0.93[ASN][1000 genomes]
rs57451017	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57755392	0.93[ASN][1000 genomes]
rs61023481	0.93[ASN][1000 genomes]
rs61455481	0.93[ASN][1000 genomes]
rs7136538	0.93[ASN][1000 genomes]
rs7136945	0.93[ASN][1000 genomes]
rs7294873	0.93[ASN][1000 genomes]
rs7295247	0.93[ASN][1000 genomes]
rs7342318	0.93[ASN][1000 genomes]
rs7342370	0.93[ASN][1000 genomes]
rs7398252	0.93[ASN][1000 genomes]
rs7975431	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49717400-49726800	Weak transcription	Right Atrium	heart
2	chr12:49717600-49723000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:49717600-49725000	Weak transcription	Pancreas	Pancrea
4	chr12:49717800-49727000	Weak transcription	Esophagus	oesophagus
5	chr12:49718000-49722800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49718000-49724600	Weak transcription	Spleen	Spleen
7	chr12:49718000-49724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:49718000-49725000	Weak transcription	Colonic Mucosa	Colon
9	chr12:49718000-49725000	Weak transcription	Fetal Heart	heart
10	chr12:49718000-49725000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:49718000-49725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:49718000-49725200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:49718000-49725200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:49718000-49725400	Weak transcription	Placenta	Placenta
15	chr12:49718000-49726200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:49718000-49726400	Weak transcription	Primary B cells from cord blood	blood
17	chr12:49718000-49730200	Weak transcription	Gastric	stomach
18	chr12:49718200-49724400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:49718200-49725200	Weak transcription	Fetal Brain Female	brain
20	chr12:49718200-49725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:49718200-49725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:49718200-49725600	Weak transcription	Fetal Kidney	kidney
23	chr12:49718400-49722800	Weak transcription	Brain Germinal Matrix	brain
24	chr12:49718400-49723800	Weak transcription	Fetal Lung	lung
25	chr12:49718400-49724200	Strong transcription	K562	blood
26	chr12:49718400-49724800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:49718400-49724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:49718600-49725000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:49718600-49725400	Strong transcription	NHEK	skin
30	chr12:49718600-49725600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:49719000-49724600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:49719200-49723800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:49719200-49724000	Strong transcription	Fetal Stomach	stomach
34	chr12:49719200-49724200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr12:49719200-49724400	Strong transcription	HepG2	liver
36	chr12:49719200-49724600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:49719200-49724600	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:49719200-49724800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:49719200-49725000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:49719200-49725000	Strong transcription	Fetal Intestine Small	intestine
41	chr12:49719200-49725200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:49719200-49725200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:49719200-49725200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:49719200-49725400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:49719200-49725400	Strong transcription	NHLF	lung
46	chr12:49719200-49725600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:49719200-49725600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:49719400-49724400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:49719400-49725400	Strong transcription	Fetal Thymus	thymus
50	chr12:49719400-49725400	Strong transcription	Thymus	Thymus

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