Variant report

Variant	rs2962500
Chromosome Location	chr5:145512951-145512952
allele	C/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	POLR2A	chr5:145512885-145513239	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:145507255..145510275-chr5:145511720..145513708,3	K562	blood:

Variant related genes	Relation type
LARS	TF binding region
ENSG00000239602	TF binding region
ENSG00000133706	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10491259	0.83[LWK][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap]
rs11948017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11953506	0.80[YRI][hapmap]
rs11960075	0.80[YRI][hapmap]
rs2063002	0.80[LWK][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap]
rs2939521	0.92[AFR][1000 genomes]
rs2939522	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2939526	1.00[AFR][1000 genomes]
rs2939534	1.00[YRI][hapmap]
rs2939536	0.91[YRI][hapmap]
rs2939537	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap]
rs2939538	1.00[YRI][hapmap]
rs2962501	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962505	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2962506	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs2962507	1.00[YRI][hapmap]
rs2962512	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap]
rs2962514	1.00[YRI][hapmap]
rs2962516	1.00[YRI][hapmap]
rs2963937	1.00[YRI][hapmap]
rs6877277	0.83[LWK][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap]
rs6884711	0.81[AFR][1000 genomes]
rs6893477	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7707229	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr5:145481200-145560200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:145490800-145535200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:145491000-145517600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:145491000-145518800	Strong transcription	Dnd41	blood
5	chr5:145491000-145542200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:145491000-145551600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:145491000-145553800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:145491000-145560200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:145491200-145518000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:145491200-145534000	Strong transcription	Osteobl	bone
11	chr5:145491200-145552600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr5:145491200-145560200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:145491200-145560200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:145491200-145560800	Weak transcription	Stomach Mucosa	stomach
15	chr5:145491400-145515400	Strong transcription	Liver	Liver
16	chr5:145491400-145516200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:145491400-145516600	Strong transcription	NH-A	brain
18	chr5:145491400-145560000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:145491400-145560400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:145491600-145557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:145491600-145559800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:145491800-145515400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:145491800-145524800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr5:145491800-145541400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:145491800-145546400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:145492000-145552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:145492200-145560200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:145494000-145520000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:145494600-145513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:145495200-145515600	Strong transcription	Primary B cells from cord blood	blood
31	chr5:145495400-145517000	Strong transcription	A549	lung
32	chr5:145495400-145517800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:145495800-145519400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:145495800-145559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:145496000-145514800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr5:145496200-145552200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:145497000-145515800	Strong transcription	Fetal Intestine Large	intestine
38	chr5:145497200-145513000	Strong transcription	Hela-S3	cervix
39	chr5:145497200-145517600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:145497600-145516000	Strong transcription	K562	blood
41	chr5:145497600-145517400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:145497600-145517800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:145499000-145557400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:145500200-145541400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:145504400-145525200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:145504800-145515800	Strong transcription	Adipose Nuclei	Adipose
47	chr5:145505400-145516400	Strong transcription	HUVEC	blood vessel
48	chr5:145505400-145531600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:145506200-145516200	Weak transcription	Psoas Muscle	Psoas
50	chr5:145506200-145523800	Weak transcription	Small Intestine	intestine

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