Variant report

Variant	rs16858936
Chromosome Location	chr3:111680599-111680600
allele	A/G
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	CTCF	chr3:111680480-111680630	HFF	foreskin:	n/a	n/a
2	CTCF	chr3:111680540-111680690	HA-sp	spinal cord:	n/a	n/a
3	POLR2A	chr3:111680560-111681151	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr3:111680207-111681258	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr3:111680480-111680630	GM12875	blood:	n/a	n/a
6	CTCF	chr3:111680560-111680710	GM12864	blood:	n/a	n/a
7	CTCF	chr3:111680540-111680690	HAc	cerebellar:	n/a	n/a
8	CTCF	chr3:111680494-111680620	GM12878	blood:	n/a	n/a
9	CTCF	chr3:111680560-111680710	GM06990	blood:	n/a	n/a
10	CTCF	chr3:111680580-111680730	GM06990	blood:	n/a	n/a
11	CTCF	chr3:111680460-111680610	HFF-Myc	foreskin:	n/a	n/a
12	CTCF	chr3:111680480-111680630	AG04449	skin:	n/a	n/a
13	POLR2A	chr3:111680230-111681594	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr3:111680145-111681358	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr3:111680212-111681193	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:111680475-111680739	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr3:111680556-111680624	GM12878	blood:	n/a	n/a
18	TCF7L2	chr3:111680453-111681117	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
PHLDB2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11713044	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1282945	0.89[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1282946	1.00[JPT][hapmap]
rs13061421	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4682066	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs493456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs579082	0.89[ASN][1000 genomes]
rs6438024	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6796683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6804475	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs712514	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs712518	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs712519	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs766745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs774744	0.89[ASN][1000 genomes]
rs9816238	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9834695	1.00[JPT][hapmap]
rs9867058	0.86[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16858936	QTRTD1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111637200-111690600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111642200-111690400	Weak transcription	Spleen	Spleen
3	chr3:111645400-111689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:111652400-111685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:111653000-111686200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:111654400-111695000	Strong transcription	Placenta	Placenta
7	chr3:111657200-111682000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:111658600-111697400	Weak transcription	Gastric	stomach
9	chr3:111658800-111685800	Weak transcription	HepG2	liver
10	chr3:111661600-111689800	Weak transcription	Ovary	ovary
11	chr3:111663000-111681400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:111663800-111681200	Strong transcription	NHEK	skin
13	chr3:111666600-111697400	Weak transcription	Esophagus	oesophagus
14	chr3:111670800-111685000	Strong transcription	Liver	Liver
15	chr3:111671000-111681800	Strong transcription	NH-A	brain
16	chr3:111671200-111680800	Weak transcription	A549	lung
17	chr3:111672800-111686000	Weak transcription	Fetal Intestine Small	intestine
18	chr3:111673000-111680600	Weak transcription	Fetal Intestine Large	intestine
19	chr3:111673000-111681800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:111673000-111682000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:111673000-111688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:111673000-111688400	Weak transcription	Fetal Stomach	stomach
23	chr3:111673000-111697400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:111673000-111697400	Weak transcription	Pancreas	Pancrea
25	chr3:111673400-111681200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:111673400-111681800	Strong transcription	Osteobl	bone
27	chr3:111673600-111686000	Weak transcription	Fetal Kidney	kidney
28	chr3:111673800-111680800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:111673800-111682000	Weak transcription	NHLF	lung
30	chr3:111675000-111680600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:111675000-111682600	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:111675000-111697400	Weak transcription	Lung	lung
33	chr3:111675800-111685200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:111676400-111681800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:111676600-111680600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:111676600-111682000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:111676800-111685800	Weak transcription	Fetal Lung	lung
38	chr3:111677200-111681600	Strong transcription	HMEC	breast
39	chr3:111677400-111680600	Weak transcription	HSMM	muscle
40	chr3:111677600-111681400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:111678000-111680600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:111678000-111682000	Weak transcription	HUVEC	blood vessel
43	chr3:111678200-111680600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:111678200-111680600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:111678200-111683400	Strong transcription	Left Ventricle	heart
46	chr3:111678200-111687800	Weak transcription	Right Ventricle	heart
47	chr3:111678200-111692800	Weak transcription	Aorta	Aorta
48	chr3:111678400-111682800	Weak transcription	HSMMtube	muscle
49	chr3:111678400-111685600	Strong transcription	Adipose Nuclei	Adipose
50	chr3:111678600-111680600	Weak transcription	Placenta Amnion	Placenta Amnion

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