Variant report

Variant	rs1403233
Chromosome Location	chr4:57885053-57885054
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	E2F4	chr4:57884979-57885241	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57882081..57885343-chr4:57886309..57891790,6	K562	blood:

Variant related genes	Relation type
POLR2B	TF binding region
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10000395	0.89[ASN][1000 genomes]
rs10020462	0.93[JPT][hapmap]
rs10023088	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.91[ASN][1000 genomes]
rs10461349	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1056364	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[ASN][1000 genomes]
rs11133470	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11573125	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11573126	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12498216	0.92[ASN][1000 genomes]
rs12506598	0.93[ASN][1000 genomes]
rs12512295	0.82[ASN][1000 genomes]
rs12621	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650737	0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1277284	0.92[CEU][hapmap];0.82[YRI][hapmap]
rs1277308	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1626594	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17087265	0.82[JPT][hapmap]
rs1713982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713983	1.00[ASN][1000 genomes]
rs1718830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs1718839	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1718863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718864	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718886	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap]
rs2276897	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293175	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2412774	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775082	0.84[ASN][1000 genomes]
rs3796531	0.81[MKK][hapmap]
rs3796532	0.91[ASN][1000 genomes]
rs3821994	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4864609	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865169	0.91[ASN][1000 genomes]
rs56763474	0.91[ASN][1000 genomes]
rs60292561	0.91[ASN][1000 genomes]
rs61337636	0.83[ASN][1000 genomes]
rs67479587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843644	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73167819	0.84[ASN][1000 genomes]
rs73167841	0.93[ASN][1000 genomes]
rs781666	0.80[CEU][hapmap];0.91[TSI][hapmap]
rs781668	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs876858	0.82[CHB][hapmap]
rs9918067	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1403233	POLR2B	cis	cerebellum	SCAN
rs1403233	POLR2B	cis	parietal	SCAN
rs1403233	IGFBP7	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
6	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
8	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
10	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
12	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:57851800-57899400	Strong transcription	Liver	Liver
15	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:57852000-57892200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:57852000-57894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:57856200-57886200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:57856800-57900000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:57858200-57899800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:57859000-57898000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57859400-57898600	Strong transcription	Dnd41	blood
30	chr4:57859600-57897800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:57860200-57898800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:57860600-57892800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:57861400-57895000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr4:57862200-57891600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:57862200-57899400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:57862200-57900000	Strong transcription	Fetal Muscle Leg	muscle
37	chr4:57862400-57886400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:57862400-57886600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:57863400-57907800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:57863600-57892000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:57865800-57886400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:57866200-57886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:57866600-57894000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:57870400-57894400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr4:57870400-57899800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr4:57870600-57886400	Strong transcription	HSMM	muscle
47	chr4:57870600-57897200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:57870600-57899000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:57870800-57885200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:57870800-57886400	Strong transcription	Adipose Nuclei	Adipose

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