Variant report

Variant	rs2274257
Chromosome Location	chr1:78429408-78429409
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	chr1:78429207-78429412	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:78423763-78431474	K562	blood:	n/a	n/a
3	POLR2A	chr1:78429000-78430009	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:78429149-78429464	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:78429123-78429472	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78428722..78431621-chr1:78443319..78444830,2	MCF-7	breast:
2	chr1:78427480..78429581-chr1:78433506..78436047,2	MCF-7	breast:

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

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1001070	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1001103	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs1001104	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10437022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10873956	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs10873960	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162390	0.82[AMR][1000 genomes]
rs11162400	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];0.96[ASN][1000 genomes]
rs11162403	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1166697	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166701	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166704	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs1166705	0.92[AMR][1000 genomes]
rs1166706	0.81[CHB][hapmap];0.92[AMR][1000 genomes]
rs1166707	0.95[AMR][1000 genomes]
rs1166709	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11805735	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807240	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]
rs12146104	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12405212	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]
rs12409561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723748	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1335481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536160	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539737	0.81[CHB][hapmap]
rs1555798	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616949	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17382996	1.00[CEU][hapmap]
rs17383213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17387365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs1971368	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136682	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2154138	0.81[CHB][hapmap];0.80[AMR][1000 genomes]
rs2296453	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];0.91[ASN][1000 genomes]
rs3767028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4370803	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4372306	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57421725	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591448	0.82[YRI][hapmap]
rs628451	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs633580	0.83[YRI][hapmap]
rs638335	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs6424640	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424650	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424660	0.80[AMR][1000 genomes]
rs6424664	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs661038	0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6656888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659045	0.83[AMR][1000 genomes]
rs6667733	0.80[AMR][1000 genomes]
rs6677890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs684579	0.86[AFR][1000 genomes]
rs7417104	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs750720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514007	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7538210	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7544892	0.80[AMR][1000 genomes]
rs9324166	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9659938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9661193	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9730688	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]

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	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
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
3	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:78406600-78436200	Strong transcription	Liver	Liver
5	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:78407000-78434400	Strong transcription	Dnd41	blood
8	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
19	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:78409600-78432000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:78409600-78432200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:78409600-78437200	Strong transcription	Hela-S3	cervix
27	chr1:78410000-78433800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:78412400-78434800	Strong transcription	Fetal Lung	lung
30	chr1:78412800-78434800	Strong transcription	Fetal Brain Female	brain
31	chr1:78413000-78432600	Strong transcription	Primary T cells from cord blood	blood
32	chr1:78415000-78434200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:78415000-78435800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:78415000-78437200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78415200-78430600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr1:78415600-78434800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr1:78415800-78432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:78415800-78434800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:78415800-78435200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:78415800-78436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:78415800-78436800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:78415800-78437600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:78415800-78440200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:78416000-78432400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:78416400-78437400	Strong transcription	K562	blood
46	chr1:78416400-78438200	Strong transcription	HMEC	breast
47	chr1:78416600-78430600	Strong transcription	NHLF	lung
48	chr1:78416600-78434800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:78416600-78435400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:78416800-78432200	Strong transcription	Thymus	Thymus

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