Variant report

Variant	rs791720
Chromosome Location	chr1:212614788-212614789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212612620..212614790-chr1:212782003..212783590,2	K562	blood:
2	chr1:212603778..212607696-chr1:212613958..212618127,5	K562	blood:

Variant related genes	Relation type
ENSG00000117691	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10863967	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10863968	0.93[ASN][1000 genomes]
rs10863969	0.85[CEU][hapmap]
rs11119937	0.99[ASN][1000 genomes]
rs11119940	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11119941	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11119943	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11119944	0.94[ASN][1000 genomes]
rs12023863	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12024457	0.84[ASN][1000 genomes]
rs3767870	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3767872	0.96[ASN][1000 genomes]
rs4951446	1.00[ASN][1000 genomes]
rs4951447	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4951448	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[ASN][1000 genomes]
rs4951598	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4951599	0.94[ASN][1000 genomes]
rs4951600	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs516961	0.93[YRI][hapmap]
rs526887	0.81[AFR][1000 genomes]
rs59001230	1.00[ASN][1000 genomes]
rs603747	0.89[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap]
rs675065	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs791720	LQK1	cis	parietal	SCAN
rs791720	DTL	cis	cerebellum	SCAN
rs791720	PIGR	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212607000-212623400	Weak transcription	HSMMtube	muscle
2	chr1:212607200-212617400	Weak transcription	Fetal Intestine Large	intestine
3	chr1:212607200-212617600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:212607400-212617600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:212607400-212617600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:212607400-212618800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:212607400-212622800	Weak transcription	Primary B cells from cord blood	blood
8	chr1:212607400-212625800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:212607400-212626000	Weak transcription	Colonic Mucosa	Colon
10	chr1:212607400-212629200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:212607600-212617600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:212607600-212617600	Weak transcription	Placenta	Placenta
13	chr1:212607600-212617800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:212607600-212618000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:212607600-212618000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:212607600-212619000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:212607600-212619000	Weak transcription	Thymus	Thymus
18	chr1:212607600-212619200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:212607600-212620600	Weak transcription	HMEC	breast
20	chr1:212607600-212621800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:212607600-212624000	Weak transcription	Fetal Brain Male	brain
22	chr1:212607600-212625800	Weak transcription	Stomach Mucosa	stomach
23	chr1:212607600-212626000	Weak transcription	NH-A	brain
24	chr1:212607800-212616800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:212607800-212617400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:212607800-212617400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:212607800-212617600	Weak transcription	Primary T cells from cord blood	blood
28	chr1:212607800-212617600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:212607800-212617600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:212607800-212617600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:212607800-212617600	Weak transcription	Right Ventricle	heart
32	chr1:212607800-212617800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:212607800-212617800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:212607800-212618800	Weak transcription	Brain Germinal Matrix	brain
35	chr1:212607800-212619200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:212607800-212619200	Weak transcription	Fetal Thymus	thymus
37	chr1:212607800-212620000	Weak transcription	Osteobl	bone
38	chr1:212607800-212623400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:212607800-212624400	Weak transcription	NHEK	skin
40	chr1:212607800-212625800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:212607800-212625800	Weak transcription	NHLF	lung
42	chr1:212607800-212629400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:212608000-212616600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:212608000-212616800	Weak transcription	Fetal Intestine Small	intestine
45	chr1:212608000-212617200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:212608000-212617400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:212608000-212617400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:212608000-212617400	Weak transcription	Liver	Liver
49	chr1:212608000-212617400	Weak transcription	Ovary	ovary
50	chr1:212608000-212617600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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