Variant report

Variant	rs13000706
Chromosome Location	chr2:46838247-46838248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46835801..46838327-chr2:46839265..46842441,5	K562	blood:
2	chr2:46834662..46838472-chr2:46842011..46844941,3	MCF-7	breast:
3	chr2:46838114..46840779-chr2:46841900..46844194,2	MCF-7	breast:
4	chr2:46835833..46838825-chr2:46842704..46844559,2	K562	blood:

Variant related genes	Relation type
ENSG00000151665	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1080871	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11894342	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12104572	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001566	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13385693	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1451153	0.88[JPT][hapmap]
rs1451156	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1531133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598517	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901263	0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap]
rs1989720	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122715	0.86[CHD][hapmap]
rs2242033	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305350	0.89[TSI][hapmap]
rs3087822	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544906	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6544907	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739397	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739468	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6752882	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7589801	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7598578	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13000706	CRIPT	cis	parietal	SCAN
rs13000706	CRIPT	cis	Stomach	GTEx
rs13000706	SOCS5	cis	multi-tissue	Pritchard
rs13000706	ATP6V1E2	cis	multi-tissue	Pritchard
rs13000706	CRIPT	cis	Esophagus Muscularis	GTEx
rs13000706	CRIPT	cis	Frontal Cortex	GTEx
rs13000706	CRIPT	cis	Temporal Cortex	GTEx
rs13000706	CRIPT	cis	multi-tissue	Pritchard
rs13000706	CRIPT	trans	brain	seeQTL
rs13000706	CRIPT	cis	brain	seeQTL
rs13000706	PIGF	cis	multi-tissue	Pritchard
rs13000706	PIGF	cis	cerebellum	SCAN
rs13000706	CRIPT	cis	Lymphoblastoid	GTEx
rs13000706	PRKCE	cis	cerebellum	SCAN
rs13000706	CRIPT	cis	lymphoblastoid	seeQTL
rs13000706	PIGF	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:46797800-46841000	Weak transcription	K562	blood
4	chr2:46802400-46842600	Weak transcription	NHEK	skin
5	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:46807800-46842400	Weak transcription	NHLF	lung
9	chr2:46807800-46842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:46807800-46842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46807800-46842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:46807800-46842800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:46807800-46842800	Weak transcription	HSMMtube	muscle
14	chr2:46807800-46843000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:46807800-46843000	Weak transcription	Fetal Stomach	stomach
16	chr2:46807800-46843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:46808000-46842800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:46808200-46838400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:46808600-46842800	Weak transcription	Placenta	Placenta
20	chr2:46809400-46842800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:46809600-46842800	Weak transcription	Fetal Thymus	thymus
22	chr2:46810600-46842600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:46811600-46842800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:46811800-46842400	Weak transcription	Osteobl	bone
25	chr2:46811800-46843000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:46812000-46842600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:46814200-46841600	Weak transcription	Fetal Heart	heart
28	chr2:46819600-46842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:46819800-46842200	Weak transcription	NHDF-Ad	bronchial
30	chr2:46824200-46842800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:46828000-46842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:46828600-46842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:46828600-46842800	Weak transcription	Left Ventricle	heart
34	chr2:46828800-46841600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:46829000-46842800	Weak transcription	Brain Angular Gyrus	brain
36	chr2:46829200-46842600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:46829800-46843200	Weak transcription	Ovary	ovary
38	chr2:46830800-46842400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:46831600-46842800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:46833600-46843200	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:46834000-46841400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:46834200-46841800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:46834200-46842600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:46834200-46842800	Weak transcription	Liver	Liver
45	chr2:46834600-46842800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:46834600-46842800	Weak transcription	Right Ventricle	heart
47	chr2:46835200-46839000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:46835200-46840000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:46835200-46842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:46835400-46838400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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