Variant report

Variant	rs7537274
Chromosome Location	chr1:214654965-214654966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10494980	0.84[CHB][hapmap]
rs10746445	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746446	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]
rs10864101	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10864102	0.92[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs11120303	1.00[ASW][hapmap]
rs11120321	1.00[CEU][hapmap]
rs11120329	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs11120330	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs11120334	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059328	1.00[ASW][hapmap]
rs12068677	0.92[CHB][hapmap]
rs12128034	0.91[CHB][hapmap]
rs12743237	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs17023030	0.83[CHB][hapmap]
rs4130486	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233305	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233306	0.84[CHB][hapmap]
rs4233307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253891	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4301608	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4421564	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4451529	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4465172	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4539105	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4655249	1.00[ASW][hapmap];0.84[TSI][hapmap]
rs4655250	0.92[CHB][hapmap]
rs4655251	0.92[CHB][hapmap]
rs4655252	0.92[CHB][hapmap]
rs4655253	0.92[CHB][hapmap]
rs4655254	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs4655255	0.91[CHB][hapmap]
rs4655347	0.92[CHB][hapmap]
rs5020616	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs5020617	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6540831	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6540835	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6540836	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540840	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665797	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6668440	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6682987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518513	0.90[CHB][hapmap]
rs7528679	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528775	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528800	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535598	1.00[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs7537159	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7555415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7537274	HHAT	cis	parietal	SCAN
rs7537274	RPS6KC1	cis	cerebellum	SCAN
rs7537274	PTPN14	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214641400-214667800	Weak transcription	Hela-S3	cervix
2	chr1:214645200-214656600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:214645800-214666000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:214646000-214672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:214647200-214661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:214648000-214669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:214649200-214660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:214650200-214657400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:214650200-214658000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:214650200-214666000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:214650600-214657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:214650800-214656400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:214650800-214657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:214650800-214660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:214650800-214662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:214651000-214655000	Weak transcription	Stomach Mucosa	stomach
17	chr1:214651000-214656200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:214651000-214656200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:214651000-214656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:214651000-214656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:214651000-214666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:214651200-214656200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:214651200-214657400	Weak transcription	Psoas Muscle	Psoas
24	chr1:214651200-214659400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:214651200-214664600	Weak transcription	Left Ventricle	heart
26	chr1:214651200-214665600	Weak transcription	NHLF	lung
27	chr1:214651200-214666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:214651200-214666400	Weak transcription	Adipose Nuclei	Adipose
29	chr1:214651400-214655600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:214651600-214656200	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:214651600-214661400	Weak transcription	Fetal Heart	heart
32	chr1:214651800-214655600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:214651800-214655800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:214651800-214655800	Weak transcription	A549	lung
35	chr1:214651800-214656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:214651800-214658000	Weak transcription	NH-A	brain
37	chr1:214651800-214663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:214651800-214665400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:214651800-214668000	Weak transcription	HSMMtube	muscle
40	chr1:214652000-214665800	Weak transcription	NHDF-Ad	bronchial
41	chr1:214652000-214666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:214652200-214658000	Weak transcription	HSMM	muscle
43	chr1:214652200-214664800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:214652400-214655400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:214652600-214656000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:214652600-214656200	Weak transcription	HMEC	breast
47	chr1:214652600-214657400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:214652600-214662000	Weak transcription	HUVEC	blood vessel
49	chr1:214654200-214656200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:214654200-214656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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