Variant report

Variant	rs3756856
Chromosome Location	chr6:35110705-35110706
allele	C/T
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	RCOR1	chr6:35110389-35110809	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr6:35110308-35110771	Hela-S3	cervix:	n/a	chr6:35110319-35110332 chr6:35110321-35110332 chr6:35110319-35110330
3	SMC3	chr6:35110359-35110734	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
TCP11	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1093986	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11552398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11961798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11964930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11969000	0.92[CEU][hapmap]
rs13196771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13203612	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13206654	0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13207848	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs13208078	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13211490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13214114	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13216424	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13217848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13219307	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16871749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16871809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16871814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896559	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1747516	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1747517	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17610836	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17611877	0.97[ASN][1000 genomes]
rs1929848	1.00[GIH][hapmap]
rs2177380	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2177382	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2395608	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2395610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2395617	1.00[GIH][hapmap]
rs2494098	0.81[ASN][1000 genomes]
rs2762336	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820225	0.84[ASN][1000 genomes]
rs34069418	0.86[ASN][1000 genomes]
rs34103100	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34208177	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34250961	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34715060	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930033	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35095464	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35106671	0.81[EUR][1000 genomes]
rs35693439	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270050	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4628094	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57111149	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66579470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67167177	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67638810	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67941146	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6899618	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913286	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913975	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6919534	1.00[GIH][hapmap]
rs6926532	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936337	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942104	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72896254	0.86[ASN][1000 genomes]
rs72897804	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72901705	0.98[ASN][1000 genomes]
rs729925	1.00[GIH][hapmap]
rs734538	1.00[GIH][hapmap];0.83[MKK][hapmap]
rs763155	1.00[GIH][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap]
rs763157	1.00[GIH][hapmap]
rs7766770	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820061	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820062	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820063	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820065	1.00[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820066	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820067	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820069	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820072	0.86[ASN][1000 genomes]
rs820077	0.88[CHD][hapmap]
rs820083	0.83[ASN][1000 genomes]
rs820095	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs820099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820100	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820101	0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820103	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs843937	0.86[ASN][1000 genomes]
rs865352	0.83[AMR][1000 genomes]
rs9394282	1.00[GIH][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs9462053	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462054	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469950	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3756856	TCP11	cis	Adipose Subcutaneous	GTEx
rs3756856	TCP11	cis	lymphoblastoid	seeQTL
rs3756856	TULP1	cis	cerebellum	SCAN
rs3756856	BRPF3	cis	cerebellum	SCAN
rs3756856	TCP11	cis	multi-tissue	Pritchard
rs3756856	TCP11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35104400-35114000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:35106000-35113600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:35106200-35113400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:35108200-35113600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:35108200-35113800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:35108200-35113800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:35108200-35114400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:35108200-35114600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:35109200-35113600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:35109200-35114000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:35109400-35110800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:35109400-35110800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:35109400-35111200	Enhancers	Hela-S3	cervix
14	chr6:35110200-35111400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:35110200-35111400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:35110200-35111400	Enhancers	Osteobl	bone
17	chr6:35110200-35117000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:35110400-35110800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:35110400-35111000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:35110400-35111200	Enhancers	HSMM	muscle
21	chr6:35110400-35111200	Enhancers	NHDF-Ad	bronchial
22	chr6:35110400-35111400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:35110400-35111400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:35110400-35111400	Enhancers	Fetal Kidney	kidney
25	chr6:35110400-35111400	Enhancers	A549	lung
26	chr6:35110600-35110800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr6:35110600-35111200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:35110600-35111400	Enhancers	HepG2	liver
29	chr6:35110600-35116000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:35110600-35116000	Weak transcription	HSMMtube	muscle

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