Variant report

Variant	rs1412867
Chromosome Location	chr1:70711236-70711237
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	POLR2A	chr1:70711052-70711794	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70709756..70712647-chr1:71546604..71549117,2	MCF-7	breast:

Variant related genes	Relation type
SRSF11	TF binding region
ENSG00000132485	Chromatin interaction
ENSG00000229956	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17131236	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17131238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17131241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34121744	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35522955	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753818	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs476591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs522320	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549843	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56299138	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56873377	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57098486	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587567	0.94[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60409157	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60598073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs610953	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61785267	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61785269	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61785270	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61785272	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs632047	0.94[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];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651717	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664084	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6664480	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666941	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6700543	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs676753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74085998	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7533067	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv871898	chr1:70681486-70723347	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' 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	14 gene(s)	inside rSNPs	diseases
4	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1412867	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs1412867	WLS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70688400-70719400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:70688600-70719800	Strong transcription	Fetal Thymus	thymus
4	chr1:70689000-70717800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr1:70689000-70718200	Strong transcription	Placenta	Placenta
6	chr1:70689200-70718600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:70689400-70719200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:70689600-70719200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:70689600-70719200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:70690200-70719800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:70690400-70719800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:70690600-70716000	Weak transcription	Stomach Mucosa	stomach
13	chr1:70690600-70719200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:70690800-70718200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:70690800-70718600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:70690800-70719200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:70691200-70717600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:70692200-70718200	Strong transcription	Primary B cells from cord blood	blood
19	chr1:70692200-70719200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr1:70692400-70717600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:70692600-70717000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:70692600-70718600	Strong transcription	NH-A	brain
23	chr1:70692800-70717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:70692800-70718000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:70692800-70719000	Strong transcription	NHDF-Ad	bronchial
26	chr1:70692800-70719200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:70693200-70718600	Strong transcription	Osteobl	bone
28	chr1:70693200-70719200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:70693400-70718000	Strong transcription	Hela-S3	cervix
30	chr1:70693400-70719000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:70693600-70714600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:70693600-70716800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:70693600-70717600	Strong transcription	HepG2	liver
34	chr1:70693600-70717800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:70693600-70718200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:70693600-70719200	Strong transcription	HUVEC	blood vessel
37	chr1:70693600-70719400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:70693600-70719600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:70693800-70718000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:70693800-70718200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:70693800-70718600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:70693800-70719200	Strong transcription	Primary T cells from cord blood	blood
43	chr1:70693800-70719200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:70693800-70719400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:70693800-70719600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:70693800-70719800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr1:70694000-70716800	Strong transcription	Fetal Lung	lung
48	chr1:70694000-70717000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:70694000-70717800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:70694000-70717800	Strong transcription	NHLF	lung

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