Variant report

Variant	rs11719458
Chromosome Location	chr3:121382005-121382006
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	chr3:121378844-121382265	K562	blood:	n/a	n/a
2	POLR2A	chr3:121381599-121382728	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121381533..121383209-chr3:121385289..121388100,2	MCF-7	breast:
2	chr3:121374281..121376977-chr3:121381116..121385045,3	MCF-7	breast:
3	chr3:121380202..121382389-chr3:121387909..121390057,2	K562	blood:

Variant related genes	Relation type
HCLS1	TF binding region
ENSG00000222057	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11706783	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11707716	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716984	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720859	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721318	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072618	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074834	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077135	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13087578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090660	0.89[EUR][1000 genomes]
rs1573819	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17691170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1920320	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2070180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs28660600	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs33988592	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34086988	0.91[EUR][1000 genomes]
rs34667636	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35988617	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36142735	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732408	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs3772130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs3805127	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs4280673	0.89[JPT][hapmap]
rs4311252	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs55643643	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55657471	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56314138	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62268732	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268734	0.92[ASN][1000 genomes]
rs66653099	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768621	0.96[CEU][hapmap]
rs6776670	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs6791046	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427165	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631939	1.00[JPT][hapmap]
rs9826473	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9839617	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9856641	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9883467	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11719458	IQCB1	cis	cerebellum	SCAN
rs11719458	HCLS1	cis	Whole Blood	GTEx
rs11719458	HEG1	cis	parietal	SCAN
rs11719458	SLC15A2	cis	cerebellum	SCAN
rs11719458	PARP9	cis	cerebellum	SCAN
rs11719458	IQCB1	cis	parietal	SCAN
rs11719458	CHST13	cis	cerebellum	SCAN
rs11719458	GOLGB1	cis	multi-tissue	Pritchard
rs11719458	EAF2	cis	cerebellum	SCAN
rs11719458	IQCB1	cis	Whole Blood	GTEx
rs11719458	IQCB1	cis	multi-tissue	Pritchard
rs11719458	CCDC58	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
2	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
3	chr3:121376400-121382200	Weak transcription	A549	lung
4	chr3:121376400-121383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
7	chr3:121378400-121383200	Weak transcription	NH-A	brain
8	chr3:121378800-121382200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:121379000-121382200	Weak transcription	NHLF	lung
10	chr3:121379000-121384200	Enhancers	Fetal Heart	heart
11	chr3:121379400-121384600	Weak transcription	Fetal Kidney	kidney
12	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
13	chr3:121379800-121382400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:121379800-121382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:121379800-121382400	Weak transcription	Ovary	ovary
16	chr3:121379800-121382400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:121379800-121382800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:121379800-121383000	Weak transcription	Esophagus	oesophagus
19	chr3:121379800-121384200	Genic enhancers	Fetal Muscle Leg	muscle
20	chr3:121380000-121382200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:121380000-121382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:121380000-121382800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:121380200-121382600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:121380200-121382800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:121380200-121385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:121380200-121386200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:121380200-121397000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:121380400-121382200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:121380400-121382400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:121380400-121382600	Weak transcription	HUVEC	blood vessel
32	chr3:121380400-121384600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:121380400-121385400	Weak transcription	K562	blood
34	chr3:121380400-121386800	Strong transcription	Brain Anterior Caudate	brain
35	chr3:121380400-121396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:121380400-121396800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:121380600-121382400	Weak transcription	Primary B cells from cord blood	blood
41	chr3:121380600-121382400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:121380600-121382400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:121380600-121382800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:121380600-121384600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:121380600-121384800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:121380600-121384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
48	chr3:121380800-121382200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:121380800-121382200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:121380800-121382200	Weak transcription	Dnd41	blood

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