Variant report

Variant	rs11586570
Chromosome Location	chr1:93305371-93305372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:93304502-93306541	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:93304614-93306685	A549	lung:	n/a	n/a
3	POLR2A	chr1:93304500-93306835	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:93304833-93305563	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:93304734-93310132	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:93303274-93305956	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:93304752-93307169	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:93304521-93305401	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:93304849-93306993	K562	blood:	n/a	n/a
10	POLR2A	chr1:93304670-93306520	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr1:93301434-93307185	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:93305026-93305574	K562	blood:	n/a	n/a
13	POLR2A	chr1:93304955-93305380	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:93304973-93305380	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:93304574-93305814	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:93304870-93306116	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:93304820-93306524	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:93304786-93305384	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:93304741-93306587	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:93303166-93307156	K562	blood:	n/a	n/a
21	POLR2A	chr1:93304645-93305387	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:93304824-93305435	K562	blood:	n/a	n/a
23	POLR2A	chr1:93301216-93310285	K562	blood:	n/a	n/a
24	POLR2A	chr1:93304502-93306489	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr1:93304981-93306782	K562	blood:	n/a	n/a
26	POLR2A	chr1:93304646-93306506	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:93304662-93310254	PFSK-1	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
2	chr1:93251020..93253744-chr1:93303793..93305482,2	K562	blood:
3	chr1:93214862..93218519-chr1:93302722..93305780,4	K562	blood:
4	chr1:93303345..93305385-chr1:93311213..93313203,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA66	TF binding region
ENSG00000122483	Chromatin interaction
ENSG00000234202	Chromatin interaction
ENSG00000207022	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10874745	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164820	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11164825	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11582791	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs11803097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062315	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081675	1.00[JPT][hapmap]
rs12082659	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731107	1.00[JPT][hapmap]
rs12738654	0.84[EUR][1000 genomes]
rs12738964	0.83[AMR][1000 genomes]
rs12743005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12746956	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	1.00[JPT][hapmap]
rs12749786	1.00[CHB][hapmap]
rs12750269	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17381426	1.00[CHB][hapmap]
rs17614449	0.85[AMR][1000 genomes]
rs1854797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255723	0.87[MKK][hapmap]
rs2263247	0.87[MKK][hapmap]
rs2481713	0.87[MKK][hapmap]
rs2811593	0.87[MKK][hapmap]
rs2893226	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34098754	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34168045	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34202284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604026	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66649041	0.85[AMR][1000 genomes]
rs6687931	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11586570	HFM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93299200-93305400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr1:93299200-93306200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:93299200-93310400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:93299400-93307200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:93299400-93309200	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:93299600-93306000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:93299600-93306600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:93299600-93309000	Weak transcription	Esophagus	oesophagus
9	chr1:93299600-93309800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:93299600-93310000	Strong transcription	Placenta	Placenta
11	chr1:93299600-93310400	Strong transcription	Fetal Thymus	thymus
12	chr1:93299800-93310600	Strong transcription	Fetal Intestine Large	intestine
13	chr1:93299800-93311600	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:93300000-93305800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:93300000-93306000	Genic enhancers	Primary T cells from cord blood	blood
16	chr1:93300000-93306200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:93300000-93309800	Strong transcription	Thymus	Thymus
18	chr1:93300000-93310000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:93300000-93310000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:93300000-93310200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:93300200-93305400	Genic enhancers	HepG2	liver
22	chr1:93300200-93306000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:93300200-93306000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:93300200-93306600	Strong transcription	Fetal Kidney	kidney
25	chr1:93300200-93308000	Strong transcription	Colonic Mucosa	Colon
26	chr1:93300200-93309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:93300200-93310000	Strong transcription	HSMMtube	muscle
28	chr1:93300200-93310200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:93300200-93310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:93300400-93305800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:93300400-93306600	Strong transcription	Lung	lung
32	chr1:93300400-93310000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:93300400-93316000	Strong transcription	Primary B cells from cord blood	blood
34	chr1:93300600-93308800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr1:93300600-93309200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:93300600-93310000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:93300800-93305600	Weak transcription	Fetal Brain Male	brain
38	chr1:93300800-93306200	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr1:93300800-93309000	Weak transcription	Spleen	Spleen
40	chr1:93300800-93310000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:93300800-93310200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:93300800-93310200	Strong transcription	HSMM	muscle
43	chr1:93300800-93310400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:93301000-93305800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:93301000-93306400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:93301000-93309600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:93301000-93309800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:93301000-93310000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:93301000-93310200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:93301000-93310200	Strong transcription	Brain Germinal Matrix	brain

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