Variant report

Variant	rs10746446
Chromosome Location	chr1:214662840-214662841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214660865..214663396-chr1:214666846..214669507,2	MCF-7	breast:
2	chr1:214660024..214663647-chr1:214669721..214672544,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10746445	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10864101	0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap]
rs10864102	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap]
rs11120321	1.00[CEU][hapmap]
rs11120329	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs11120330	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs11120334	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12068677	0.83[CHB][hapmap]
rs12128034	0.82[CHB][hapmap]
rs12743237	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4130486	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233305	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233307	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253891	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4301608	1.00[CEU][hapmap]
rs4421564	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451529	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4465172	1.00[CEU][hapmap];0.86[CHD][hapmap]
rs4539105	0.87[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4655250	0.83[CHB][hapmap]
rs4655251	0.83[CHB][hapmap]
rs4655252	0.83[CHB][hapmap]
rs4655253	0.83[CHB][hapmap]
rs4655254	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4655255	0.82[CHB][hapmap]
rs4655347	0.83[CHB][hapmap]
rs5020616	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs5020617	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6540831	1.00[CEU][hapmap]
rs6540835	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6540836	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6540839	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6540840	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665797	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668440	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6682987	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518513	0.81[CHB][hapmap]
rs7528679	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528775	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528800	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535598	1.00[CEU][hapmap]
rs7537274	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555415	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10746446	RPS6KC1	cis	cerebellum	SCAN
rs10746446	PTPN14	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214641400-214667800	Weak transcription	Hela-S3	cervix
2	chr1:214645800-214666000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:214646000-214672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:214648000-214669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:214650200-214666000	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:214651000-214666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:214651200-214664600	Weak transcription	Left Ventricle	heart
8	chr1:214651200-214665600	Weak transcription	NHLF	lung
9	chr1:214651200-214666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:214651200-214666400	Weak transcription	Adipose Nuclei	Adipose
11	chr1:214651800-214663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:214651800-214665400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:214651800-214668000	Weak transcription	HSMMtube	muscle
14	chr1:214652000-214665800	Weak transcription	NHDF-Ad	bronchial
15	chr1:214652000-214666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:214652200-214664800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:214654400-214677400	Weak transcription	Gastric	stomach
18	chr1:214656800-214664600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:214656800-214665800	Weak transcription	HMEC	breast
20	chr1:214656800-214667800	Weak transcription	A549	lung
21	chr1:214658400-214665000	Weak transcription	NH-A	brain
22	chr1:214658600-214668000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:214658800-214666200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:214658800-214667600	Weak transcription	HSMM	muscle
25	chr1:214659800-214663200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:214659800-214665800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:214660000-214663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:214660000-214664600	Weak transcription	Osteobl	bone
29	chr1:214660200-214664600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:214660200-214664800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:214660200-214664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:214660200-214667800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:214660200-214667800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:214660200-214668000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:214660400-214663000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:214660600-214665200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:214661000-214666000	Strong transcription	NHEK	skin
38	chr1:214661000-214666400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:214661200-214663200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:214661200-214666200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:214661400-214663200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr1:214661400-214664800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:214661400-214665800	Weak transcription	Ovary	ovary
44	chr1:214661400-214666400	Weak transcription	Right Atrium	heart
45	chr1:214661400-214667800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:214661600-214663000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:214661600-214663200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:214661600-214663400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:214662000-214663200	Strong transcription	HUVEC	blood vessel
50	chr1:214662000-214664800	Weak transcription	Aorta	Aorta

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