Variant report

Variant	rs12405212
Chromosome Location	chr1:78415271-78415272
allele	A/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	chr1:78414812-78418855	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78411683..78415390-chr1:78442833..78445980,4	MCF-7	breast:

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000137960	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001070	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1001103	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1001104	0.80[AMR][1000 genomes]
rs10437022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873956	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10873960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162403	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162406	0.81[AMR][1000 genomes]
rs1166697	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166704	0.81[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1166705	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1166706	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1166707	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs1166709	0.81[CHB][hapmap]
rs11805735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146104	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12409561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723748	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1536160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539737	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1555798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1616949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1626757	0.82[AMR][1000 genomes]
rs17382996	1.00[CEU][hapmap]
rs17383213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17387365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1855704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1971368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2136682	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154138	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2274257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3767028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370803	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4372306	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57421725	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628451	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs638335	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs6424640	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6424650	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424660	0.84[AMR][1000 genomes]
rs6424664	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs661038	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs6656888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6659045	0.80[AMR][1000 genomes]
rs6667733	0.80[AMR][1000 genomes]
rs6677890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs7417104	0.81[CHB][hapmap]
rs750720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514007	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs7538210	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7544892	0.80[AMR][1000 genomes]
rs9324166	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9659938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9661193	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9730688	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
2	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:78388600-78416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:78392200-78420400	Strong transcription	HSMM	muscle
5	chr1:78393000-78418600	Weak transcription	Lung	lung
6	chr1:78393200-78417400	Weak transcription	Small Intestine	intestine
7	chr1:78393400-78418000	Weak transcription	Stomach Mucosa	stomach
8	chr1:78396800-78415800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:78396800-78419600	Weak transcription	Ovary	ovary
10	chr1:78397800-78418600	Weak transcription	Spleen	Spleen
11	chr1:78398600-78418400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:78400400-78417200	Weak transcription	Gastric	stomach
13	chr1:78400600-78415800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:78403000-78418800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:78403200-78415800	Weak transcription	Fetal Stomach	stomach
16	chr1:78405000-78418600	Weak transcription	Aorta	Aorta
17	chr1:78405200-78417800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:78405600-78415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:78405800-78416600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
22	chr1:78406000-78420200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:78406000-78426600	Weak transcription	Fetal Heart	heart
24	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:78406600-78436200	Strong transcription	Liver	Liver
26	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:78407000-78434400	Strong transcription	Dnd41	blood
29	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:78407200-78415800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:78407400-78427600	Strong transcription	Fetal Intestine Large	intestine
32	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:78407600-78417000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:78407800-78420400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
44	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:78408600-78417800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:78409200-78415800	Weak transcription	Thymus	Thymus

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