Variant report

Variant	rs1342650
Chromosome Location	chr1:113934304-113934305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:
2	chr1:113248698..113251078-chr1:113932422..113935147,2	MCF-7	breast:
3	chr1:113933188..113935605-chr6:26055289..26057331,2	MCF-7	breast:
4	chr1:113933924..113934739-chr1:113995326..113996059,2	MCF-7	breast:
5	chr1:113932215..113934552-chr4:83350688..83352314,2	MCF-7	breast:
6	chr1:113931908..113934535-chr17:56707476..56709297,2	MCF-7	breast:
7	chr1:113256258..113258254-chr1:113933817..113936025,2	K562	blood:

Variant related genes	Relation type
ENSG00000145293	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000232499	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000152795	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12071016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12132889	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12354140	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12739961	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];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1342652	0.92[MEX][hapmap]
rs17507114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935747	0.92[MEX][hapmap]
rs2186051	0.92[ASN][1000 genomes]
rs2359412	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6685909	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6688796	0.84[ASN][1000 genomes]
rs71662825	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71662826	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1342650	KIAA1324	cis	parietal	SCAN
rs1342650	AP4B1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113931200-113934400	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:113931200-113935600	Active TSS	NHDF-Ad	bronchial
3	chr1:113931200-113937200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:113931400-113934400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:113931400-113934800	Active TSS	Gastric	stomach
6	chr1:113931400-113934800	Active TSS	Left Ventricle	heart
7	chr1:113931400-113934800	Active TSS	Pancreas	Pancrea
8	chr1:113931400-113935000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:113931400-113935000	Active TSS	A549	lung
10	chr1:113931600-113934400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:113931600-113934800	Active TSS	Right Ventricle	heart
12	chr1:113931600-113934800	Bivalent/Poised TSS	HepG2	liver
13	chr1:113931600-113935000	Active TSS	Stomach Mucosa	stomach
14	chr1:113931600-113935400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:113931600-113935400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:113931600-113935600	Active TSS	Aorta	Aorta
17	chr1:113931600-113935600	Active TSS	Colonic Mucosa	Colon
18	chr1:113931600-113935600	Active TSS	Ovary	ovary
19	chr1:113931600-113936000	Active TSS	Right Atrium	heart
20	chr1:113931600-113937600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:113931800-113934400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr1:113931800-113936000	Active TSS	Colon Smooth Muscle	Colon
23	chr1:113931800-113937400	Active TSS	Fetal Intestine Large	intestine
24	chr1:113932000-113934400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr1:113932000-113934400	Active TSS	Psoas Muscle	Psoas
26	chr1:113932000-113934600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:113932000-113934800	Active TSS	Esophagus	oesophagus
28	chr1:113932000-113934800	Active TSS	Lung	lung
29	chr1:113932000-113935200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:113932000-113935400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:113932200-113934400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:113932200-113934400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:113932200-113934400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:113932200-113934400	Active TSS	NHLF	lung
35	chr1:113932200-113934600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:113932200-113934800	Active TSS	Small Intestine	intestine
37	chr1:113932200-113937200	Active TSS	Fetal Intestine Small	intestine
38	chr1:113932400-113934400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:113932400-113934400	Active TSS	Hela-S3	cervix
40	chr1:113932400-113934400	Active TSS	HSMM	muscle
41	chr1:113932400-113934400	Active TSS	HSMMtube	muscle
42	chr1:113932400-113934800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:113932400-113935000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr1:113932400-113935000	Active TSS	HMEC	breast
45	chr1:113932400-113935600	Active TSS	Brain Angular Gyrus	brain
46	chr1:113932400-113935600	Active TSS	Fetal Stomach	stomach
47	chr1:113932400-113936200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:113932600-113934400	Active TSS	Liver	Liver
49	chr1:113933200-113934600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:113933400-113934400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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