Variant report

Variant	rs791504
Chromosome Location	chr1:224694877-224694878
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224693369..224695979-chr1:224697952..224700518,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753474	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs10916626	0.81[ASN][1000 genomes]
rs10916628	0.91[EUR][1000 genomes]
rs10916629	0.84[EUR][1000 genomes]
rs10916631	0.88[EUR][1000 genomes]
rs10916632	0.88[EUR][1000 genomes]
rs12093242	0.88[EUR][1000 genomes]
rs12140117	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12140906	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141016	0.99[ASN][1000 genomes]
rs12141708	0.88[EUR][1000 genomes]
rs12142949	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12566578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1891243	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1891244	0.96[EUR][1000 genomes]
rs2648743	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738367	0.88[EUR][1000 genomes]
rs4294381	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap]
rs4653589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59319739	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61825792	0.96[EUR][1000 genomes]
rs6426133	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665956	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6688146	0.90[EUR][1000 genomes]
rs6695773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699035	0.88[EUR][1000 genomes]
rs712065	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712066	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541723	0.88[EUR][1000 genomes]
rs7541917	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7545252	0.91[EUR][1000 genomes]
rs7550648	0.88[EUR][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv947162	chr1:224690408-224695941	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs791504	BPNT1	cis	parietal	SCAN
rs791504	CNIH3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224685200-224695800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:224690000-224699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:224690000-224702000	Enhancers	Liver	Liver
4	chr1:224690200-224697200	Weak transcription	Gastric	stomach
5	chr1:224691800-224695000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:224691800-224695600	Weak transcription	Small Intestine	intestine
7	chr1:224691800-224698400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:224692000-224696000	Weak transcription	Fetal Kidney	kidney
9	chr1:224692000-224697000	Weak transcription	GM12878-XiMat	blood
10	chr1:224692000-224697400	Weak transcription	Fetal Stomach	stomach
11	chr1:224692000-224697400	Enhancers	HepG2	liver
12	chr1:224692000-224698400	Weak transcription	HSMM	muscle
13	chr1:224692000-224698400	Weak transcription	HSMMtube	muscle
14	chr1:224692000-224701600	Weak transcription	Fetal Lung	lung
15	chr1:224692400-224697800	Weak transcription	Placenta	Placenta
16	chr1:224692400-224701600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:224692600-224695200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:224692600-224695200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:224692600-224695600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:224692600-224695800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:224692600-224697000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:224692600-224697200	Weak transcription	Fetal Thymus	thymus
23	chr1:224692600-224697200	Weak transcription	Stomach Mucosa	stomach
24	chr1:224692600-224697400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:224692600-224698800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:224692600-224700600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:224693000-224695800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:224693000-224697200	Weak transcription	Lung	lung
29	chr1:224693000-224697200	Weak transcription	Dnd41	blood
30	chr1:224693000-224698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:224693200-224697000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:224693200-224697200	Weak transcription	K562	blood
33	chr1:224693400-224696600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:224693600-224695800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:224693600-224699200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:224694000-224696400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:224694200-224695200	Weak transcription	Brain Germinal Matrix	brain
38	chr1:224694200-224697200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:224694200-224704000	Weak transcription	Right Atrium	heart
40	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
42	chr1:224694400-224695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:224694400-224695400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:224694400-224695800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:224694400-224695800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:224694400-224697000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:224694400-224697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:224694400-224697200	Weak transcription	NHLF	lung
49	chr1:224694400-224697400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:224694400-224697800	Weak transcription	Esophagus	oesophagus

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