Variant report

Variant	rs2582790
Chromosome Location	chr1:120314849-120314850
allele	A/C/G/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	RFX5	chr1:120314691-120315197	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120307009..120310349-chr1:120312999..120315944,3	K562	blood:
3	chr1:120312850..120316176-chr1:120320921..120324121,3	MCF-7	breast:
4	chr1:120307185..120310919-chr1:120314740..120318225,4	MCF-7	breast:

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

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1163542	0.97[EUR][1000 genomes]
rs1163543	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1163544	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1163550	0.97[EUR][1000 genomes]
rs1177389	0.98[EUR][1000 genomes]
rs12132674	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs1814447	1.00[EUR][1000 genomes]
rs2282402	0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2582779	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582780	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582782	0.98[EUR][1000 genomes]
rs2582784	0.95[CEU][hapmap]
rs2582785	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582786	0.94[CEU][hapmap];1.00[EUR][1000 genomes]
rs2843014	0.98[EUR][1000 genomes]
rs2843015	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843016	0.96[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs2843017	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72695189	0.95[EUR][1000 genomes]
rs753425	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs930448	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs935060	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978730	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs2582790	CD2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120309800-120316000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:120310000-120316200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:120310000-120316600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:120310200-120316200	Weak transcription	Psoas Muscle	Psoas
5	chr1:120310400-120315400	Weak transcription	Hela-S3	cervix
6	chr1:120311600-120318800	Enhancers	Fetal Intestine Large	intestine
7	chr1:120311800-120315800	Enhancers	Liver	Liver
8	chr1:120311800-120315800	Weak transcription	Fetal Heart	heart
9	chr1:120311800-120316200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:120311800-120316200	Weak transcription	Left Ventricle	heart
11	chr1:120311800-120316400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:120311800-120316400	Weak transcription	Ovary	ovary
13	chr1:120311800-120317800	Enhancers	HepG2	liver
14	chr1:120311800-120319600	Enhancers	Fetal Intestine Small	intestine
15	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:120311800-120325400	Weak transcription	Lung	lung
17	chr1:120312000-120315600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:120312000-120316400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:120312000-120316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:120312000-120318600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:120312200-120316200	Weak transcription	Gastric	stomach
22	chr1:120312400-120315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:120312400-120316000	Weak transcription	Right Ventricle	heart
24	chr1:120312600-120316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:120313400-120317400	Enhancers	Fetal Lung	lung
26	chr1:120314200-120315400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:120314200-120315400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:120314200-120316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:120314200-120316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:120314200-120316200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:120314400-120315600	Weak transcription	Stomach Mucosa	stomach
32	chr1:120314400-120315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:120314400-120315800	Weak transcription	Placenta	Placenta
34	chr1:120314400-120315800	Weak transcription	Small Intestine	intestine
35	chr1:120314400-120316200	Weak transcription	Esophagus	oesophagus
36	chr1:120314400-120316200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:120314400-120316200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:120314400-120316200	Weak transcription	Pancreas	Pancrea
39	chr1:120314400-120316200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:120314400-120318000	Weak transcription	Colonic Mucosa	Colon
41	chr1:120314400-120322600	Weak transcription	Right Atrium	heart
42	chr1:120314600-120315800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:120314600-120315800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:120314600-120321800	Weak transcription	Fetal Stomach	stomach
45	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:120314800-120315200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:120314800-120315200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:120314800-120316000	Weak transcription	Fetal Kidney	kidney

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