Variant report

Variant	rs2293175
Chromosome Location	chr4:57861358-57861359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57860298..57862762-chr4:57864153..57866131,2	K562	blood:
2	chr4:57854152..57858062-chr4:57860294..57862898,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1056364	0.81[MKK][hapmap]
rs11133470	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12621	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs1277284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1277287	0.81[TSI][hapmap]
rs1277308	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs1277311	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap]
rs1403233	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1625691	0.81[TSI][hapmap]
rs1626594	0.81[EUR][1000 genomes]
rs1713982	0.81[EUR][1000 genomes]
rs1713997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1718830	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1718831	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1718837	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs1718839	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs1718863	0.81[EUR][1000 genomes]
rs1718864	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1718878	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1718882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1718886	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412772	1.00[JPT][hapmap]
rs2412774	0.80[EUR][1000 genomes]
rs2948348	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35982175	0.80[ASN][1000 genomes]
rs3796531	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.89[ASN][1000 genomes]
rs4864609	0.81[EUR][1000 genomes]
rs67479587	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6841086	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs6843644	0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs7668814	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs781666	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs781668	0.88[CEU][hapmap];0.91[TSI][hapmap]

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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv964049	chr4:57858281-57871268	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2293175	POLR2B	cis	parietal	SCAN
rs2293175	POLR2B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:57847000-57861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:57848000-57861400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:57848400-57875200	Weak transcription	Stomach Mucosa	stomach
8	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:57849200-57869000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:57849600-57884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:57849800-57861400	Weak transcription	Psoas Muscle	Psoas
14	chr4:57850600-57870200	Strong transcription	GM12878-XiMat	blood
15	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
16	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
18	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
20	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:57851600-57861400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:57851600-57861400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:57851600-57864400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
25	chr4:57851800-57861400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:57851800-57861400	Strong transcription	Adipose Nuclei	Adipose
27	chr4:57851800-57863400	Strong transcription	Primary hematopoietic stem cells	blood
28	chr4:57851800-57868600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:57851800-57899400	Strong transcription	Liver	Liver
32	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:57852000-57892200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:57852000-57894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:57854000-57861400	Weak transcription	Brain Angular Gyrus	brain
40	chr4:57854400-57861400	Weak transcription	Spleen	Spleen
41	chr4:57854600-57861400	Weak transcription	Fetal Lung	lung
42	chr4:57855400-57861400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:57856000-57861400	Weak transcription	Gastric	stomach
44	chr4:57856000-57861400	Weak transcription	Pancreas	Pancrea
45	chr4:57856000-57861600	Weak transcription	Ovary	ovary
46	chr4:57856000-57868400	Strong transcription	HMEC	breast
47	chr4:57856000-57870800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:57856000-57871800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:57856200-57866000	Weak transcription	Right Ventricle	heart

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