Variant report

Variant	rs12621
Chromosome Location	chr4:57897570-57897571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10000395	0.87[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];0.86[MKK][hapmap];0.89[ASN][1000 genomes]
rs10461349	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1056364	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.89[ASN][1000 genomes]
rs11133470	0.88[EUR][1000 genomes]
rs11573125	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11573126	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12498216	0.90[ASN][1000 genomes]
rs12506598	0.92[ASN][1000 genomes]
rs12512295	0.81[ASN][1000 genomes]
rs12650737	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1277284	0.92[CEU][hapmap]
rs1277308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403233	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]
rs1626594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17087265	0.82[JPT][hapmap]
rs1713982	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1713983	0.98[ASN][1000 genomes]
rs1718830	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718831	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]
rs1718837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs1718839	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1718863	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718864	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718878	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718886	0.92[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs2276897	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293175	0.80[EUR][1000 genomes]
rs2412774	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775082	0.82[ASN][1000 genomes]
rs3796532	0.93[ASN][1000 genomes]
rs3821994	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4864609	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865169	0.89[ASN][1000 genomes]
rs56763474	0.93[ASN][1000 genomes]
rs60292561	0.93[ASN][1000 genomes]
rs61337636	0.81[ASN][1000 genomes]
rs67479587	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73167819	0.82[ASN][1000 genomes]
rs73167841	0.92[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	0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12621	POLR2B	cis	cerebellum	SCAN
rs12621	POLR2B	cis	parietal	SCAN

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	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
5	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
7	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
9	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:57851800-57899400	Strong transcription	Liver	Liver
12	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:57856800-57900000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr4:57858200-57899800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:57859000-57898000	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr4:57859400-57898600	Strong transcription	Dnd41	blood
24	chr4:57859600-57897800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:57860200-57898800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:57862200-57899400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:57862200-57900000	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:57863400-57907800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:57870400-57899800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr4:57870600-57899000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr4:57871000-57899600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:57871800-57897800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:57879400-57899800	Strong transcription	Fetal Kidney	kidney
34	chr4:57883200-57898000	Strong transcription	Brain Germinal Matrix	brain
35	chr4:57883200-57899600	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:57885600-57898200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:57885800-57898200	Strong transcription	Fetal Lung	lung
38	chr4:57887000-57900000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:57887000-57900200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:57887200-57899800	Strong transcription	Adipose Nuclei	Adipose
41	chr4:57887200-57900000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:57887400-57900400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:57888000-57898800	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr4:57889000-57897600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:57889000-57910200	Weak transcription	Esophagus	oesophagus
46	chr4:57889600-57899400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:57889800-57899600	Strong transcription	HMEC	breast
48	chr4:57889800-57899800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:57889800-57900000	Strong transcription	HSMMtube	muscle
50	chr4:57889800-57900000	Strong transcription	HUVEC	blood vessel

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