Variant report

Variant	rs753424
Chromosome Location	chr1:120316166-120316167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:120315969-120317021	HEK293	kidney:	n/a	n/a
2	POLR2A	chr1:120315959-120316296	MCF10A-Er-Src	breast:	n/a	n/a
3	KAP1	chr1:120316066-120316995	U2OS	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:120316152-120316202	ECC-1	luminal epithelium:	n/a
2	chr1:120316152-120316202	IMR90	lung:	fetal
3	chr1:120316152-120316202	ProgFib	skin:	n/a
4	chr1:120316152-120316202	SK-N-SH	brain:	n/a
5	chr1:120316152-120316202	ovcar-3	ovarian:	n/a
6	chr1:120316152-120316202	HNPCEpiC	eye:	n/a
7	chr1:120316152-120316202	GM12878	blood:	n/a
8	chr1:120316152-120316202	GM19239	blood:	n/a
9	chr1:120316152-120316202	AG09319	gingival:	n/a
10	chr1:120316152-120316202	HPAEpiC	pulmonary alveolar:	n/a
11	chr1:120316152-120316202	PrEC	prostate:	n/a
12	chr1:120316152-120316202	HRCEpiC	kidney:	n/a
13	chr1:120316152-120316202	SK-N-MC	brain:	n/a
14	chr1:120316152-120316202	AG04450	lung:	fetal
15	chr1:120316152-120316202	K562	blood:	n/a
16	chr1:120316152-120316202	Hela-S3	cervix:	n/a
17	chr1:120316152-120316202	HUVEC	blood vessel:	n/a
18	chr1:120316152-120316202	HMEC	breast:	n/a
19	chr1:120316152-120316202	PANC-1	pancreas:	n/a
20	chr1:120316152-120316202	Hepatocyte	liver:	n/a
21	chr1:120316152-120316202	Caco-2	colon:	n/a
22	chr1:120316152-120316202	HRE	kidney:	n/a
23	chr1:120316152-120316202	AG10803	skin:	n/a
24	chr1:120316152-120316202	GM12891	blood:	n/a
25	chr1:120316152-120316202	LNCaP	prostate:	n/a
26	chr1:120316152-120316202	Jurkat	blood:	n/a
27	chr1:120316152-120316202	HCM	heart:	n/a
28	chr1:120316152-120316202	NT2-D1	testis:	n/a
29	chr1:120316152-120316202	T-47D	breast:	n/a
30	chr1:120316152-120316202	CMK	blood:	n/a
31	chr1:120316152-120316202	NHBE	bronchial:	n/a
32	chr1:120316152-120316202	SKMC	muscle:	n/a
33	chr1:120316152-120316202	HEK293	kidney:	embryo
34	chr1:120316152-120316202	HCF	heart:	n/a
35	chr1:120316152-120316202	NH-A	brain:	n/a
36	chr1:120316152-120316202	AG04449	skin:	fetal
37	chr1:120316152-120316202	BJ	skin:	n/a
38	chr1:120316152-120316202	AoSMC	blood vessel:	n/a
39	chr1:120316152-120316202	HepG2	liver:	n/a
40	chr1:120316152-120316202	SK-N-SH_RA	brain:	n/a
41	chr1:120316152-120316202	AG09309	skin:	n/a
42	chr1:120316152-120316202	SAEC	small airway:	n/a
43	chr1:120316152-120316202	GM06990	blood:	n/a
44	chr1:120316152-120316202	HEEpiC	esophagus:	n/a
45	chr1:120316152-120316202	HAEpiC	amniotic membrane:	n/a
46	chr1:120316152-120316202	GM12892	blood:	n/a
47	chr1:120316152-120316202	MCF10A-Er-Src	breast:	n/a
48	chr1:120316152-120316202	RPTEC	kidney:	n/a
49	chr1:120316152-120316202	HIPEpiC	eye:	n/a
50	chr1:120316152-120316202	H1-hESC	embryonic stem cell:	embryo

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120315172..120317615-chr17:59486307..59488935,2	MCF-7	breast:
2	chr1:120312850..120316176-chr1:120320921..120324121,3	MCF-7	breast:
3	chr1:120315709..120317268-chr1:120336953..120338874,2	MCF-7	breast:
4	chr1:120307185..120310919-chr1:120314740..120318225,4	MCF-7	breast:

No data

Variant related genes	Relation type
HMGCS2	TF binding region
HMGCS2	CpG island
ENSG00000134240	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10494231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1052972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10737757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737758	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10737759	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10737760	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10754420	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10754421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10754422	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10754423	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10754424	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10802134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10802135	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10802136	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10802137	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10923900	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10923903	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10923904	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10923905	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1163545	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12047532	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12566808	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12567027	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12567029	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12730035	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12747679	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1441006	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1441007	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1441012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1441013	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1530227	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1539071	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1539074	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1539075	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17258467	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119470	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2282403	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2582783	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4659236	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4659237	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6428842	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6661517	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6683871	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6689072	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697347	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698813	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6698907	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs699778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs729234	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7516324	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs935056	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs935057	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs935059	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs947270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs947271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs753424	HMGCS2	cis	lung	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120310000-120316200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:120310000-120316600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:120310200-120316200	Weak transcription	Psoas Muscle	Psoas
4	chr1:120311600-120318800	Enhancers	Fetal Intestine Large	intestine
5	chr1:120311800-120316200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:120311800-120316200	Weak transcription	Left Ventricle	heart
7	chr1:120311800-120316400	Weak transcription	Adipose Nuclei	Adipose
8	chr1:120311800-120316400	Weak transcription	Ovary	ovary
9	chr1:120311800-120317800	Enhancers	HepG2	liver
10	chr1:120311800-120319600	Enhancers	Fetal Intestine Small	intestine
11	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:120311800-120325400	Weak transcription	Lung	lung
13	chr1:120312000-120316400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:120312000-120316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:120312000-120318600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:120312200-120316200	Weak transcription	Gastric	stomach
17	chr1:120313400-120317400	Enhancers	Fetal Lung	lung
18	chr1:120314200-120316200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:120314400-120316200	Weak transcription	Esophagus	oesophagus
20	chr1:120314400-120316200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:120314400-120316200	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:120314400-120316200	Weak transcription	Pancreas	Pancrea
23	chr1:120314400-120316200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:120314400-120318000	Weak transcription	Colonic Mucosa	Colon
25	chr1:120314400-120322600	Weak transcription	Right Atrium	heart
26	chr1:120314600-120321800	Weak transcription	Fetal Stomach	stomach
27	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:120315200-120317000	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:120315200-120318400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:120315400-120316200	Enhancers	Hela-S3	cervix
31	chr1:120315400-120317000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:120315400-120318000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:120315600-120316400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:120315600-120317800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:120315600-120318400	Enhancers	Stomach Mucosa	stomach
36	chr1:120315800-120316200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:120315800-120316400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr1:120315800-120316400	Flanking Active TSS	Liver	Liver
39	chr1:120315800-120316600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:120315800-120316800	Enhancers	Placenta	Placenta
41	chr1:120315800-120316800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:120315800-120316800	Enhancers	Small Intestine	intestine
43	chr1:120315800-120317000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:120315800-120317200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:120315800-120317200	Enhancers	Fetal Heart	heart
46	chr1:120315800-120318200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:120315800-120322000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:120316000-120316200	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr1:120316000-120316200	Bivalent Enhancer	Osteobl	bone
50	chr1:120316000-120316600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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