Variant report

Variant	rs3741624
Chromosome Location	chr12:49432263-49432264
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	POLR2A	chr12:49431484-49432384	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:49432226-49432263	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:49430737-49432401	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:49431222-49432546	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:49430548-49432264	K562	blood:	n/a	n/a
6	POLR2A	chr12:49432232-49432377	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:49430781-49432410	HL-60	blood:	n/a	n/a
8	POLR2A	chr12:49430756-49432327	K562	blood:	n/a	n/a
9	POLR2A	chr12:49430567-49432340	K562	blood:	n/a	n/a
10	POLR2A	chr12:49431517-49432376	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49432057..49433907-chr12:49523639..49525238,2	K562	blood:
2	chr12:49411035..49414032-chr12:49431081..49434275,3	K562	blood:

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000181929	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10459219	1.00[LWK][hapmap]
rs11610308	1.00[CHB][hapmap]
rs11833860	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs12318558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12321484	1.00[LWK][hapmap];1.00[MEX][hapmap]
rs12424638	1.00[CHB][hapmap]
rs12809774	1.00[LWK][hapmap]
rs2024	1.00[LWK][hapmap]
rs7311091	1.00[JPT][hapmap]
rs833823	1.00[CHB][hapmap]
rs833836	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49413000-49453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49413400-49449000	Strong transcription	Fetal Intestine Small	intestine
3	chr12:49413800-49444000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:49413800-49449200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:49414200-49449000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:49414400-49443000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:49414400-49443600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:49414400-49448800	Strong transcription	Colonic Mucosa	Colon
9	chr12:49414400-49449000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:49414400-49449000	Strong transcription	Brain Cingulate Gyrus	brain
11	chr12:49414400-49449000	Strong transcription	Brain Germinal Matrix	brain
12	chr12:49414400-49449200	Strong transcription	Fetal Stomach	stomach
13	chr12:49414400-49449200	Strong transcription	Fetal Thymus	thymus
14	chr12:49414400-49449200	Strong transcription	Thymus	Thymus
15	chr12:49414400-49449400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:49414400-49449400	Strong transcription	Fetal Intestine Large	intestine
17	chr12:49414400-49449800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:49414600-49433000	Strong transcription	Placenta	Placenta
19	chr12:49414600-49439600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:49414600-49442600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:49414600-49443200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:49414600-49443200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr12:49414600-49448600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:49414600-49448600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:49414600-49448600	Strong transcription	Adipose Nuclei	Adipose
26	chr12:49414600-49448800	Strong transcription	Ovary	ovary
27	chr12:49414600-49449000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:49414600-49449000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:49414600-49449000	Strong transcription	Primary T cells from cord blood	blood
30	chr12:49414600-49449400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:49414600-49449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:49414600-49449800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:49414800-49435400	Strong transcription	A549	lung
34	chr12:49414800-49447200	Strong transcription	Dnd41	blood
35	chr12:49414800-49448200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:49414800-49449200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:49414800-49449200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:49414800-49449400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:49414800-49449400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:49415000-49442800	Strong transcription	NHEK	skin
41	chr12:49415000-49449000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:49415000-49449000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:49415000-49449000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:49415200-49443200	Strong transcription	HUVEC	blood vessel
45	chr12:49415200-49443200	Strong transcription	Osteobl	bone
46	chr12:49415200-49448600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:49415200-49448600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:49415200-49448800	Strong transcription	Liver	Liver
49	chr12:49415200-49449600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:49415400-49443000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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