Variant report

Variant	rs1724125
Chromosome Location	chr2:96831355-96831356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96828939..96831395-chr2:96833381..96835868,2	K562	blood:
2	chr2:96785911..96788186-chr2:96829635..96832570,2	K562	blood:
3	chr2:96818239..96820649-chr2:96830872..96833353,2	K562	blood:
4	chr2:96820286..96828646-chr2:96829192..96834775,11	K562	blood:
5	chr2:96804543..96806580-chr2:96830322..96833179,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CIAO1-3	chr2:96830924-96831512	expReg_chr2_7288_+

No data

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10183151	0.89[EUR][1000 genomes]
rs1030864	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168965	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1168966	0.81[EUR][1000 genomes]
rs1168967	0.81[EUR][1000 genomes]
rs1168968	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168970	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168972	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168974	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168976	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11693248	0.81[EUR][1000 genomes]
rs1724121	0.83[EUR][1000 genomes]
rs2140938	0.82[EUR][1000 genomes]
rs2229169	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2312955	0.91[EUR][1000 genomes]
rs2576437	0.82[EUR][1000 genomes]
rs2579549	0.83[EUR][1000 genomes]
rs2579550	0.84[EUR][1000 genomes]
rs2579552	0.85[EUR][1000 genomes]
rs2692893	0.86[EUR][1000 genomes]
rs2692894	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2692934	0.84[EUR][1000 genomes]
rs2692936	0.84[EUR][1000 genomes]
rs2692937	0.85[EUR][1000 genomes]
rs2917662	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2969490	0.82[EUR][1000 genomes]
rs2969491	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3111873	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3821051	0.83[EUR][1000 genomes]
rs4907299	0.88[EUR][1000 genomes]
rs58448550	0.81[EUR][1000 genomes]
rs749457	0.81[EUR][1000 genomes]
rs7561198	0.91[EUR][1000 genomes]
rs7604842	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
8	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1724125	FAHD2CP	cis	lung	GTEx
rs1724125	GPAT2	cis	Muscle Skeletal	GTEx
rs1724125	ADRA2B	cis	Nerve Tibial	GTEx
rs1724125	ADRA2B	cis	Thyroid	GTEx
rs1724125	FAHD2CP	cis	Muscle Skeletal	GTEx
rs1724125	GPAT2	cis	Adipose Subcutaneous	GTEx
rs1724125	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96814400-96840000	Weak transcription	Right Atrium	heart
2	chr2:96821000-96831800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:96827600-96831400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:96827600-96831600	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:96827600-96831600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:96828200-96832800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:96828200-96833400	Weak transcription	Stomach Mucosa	stomach
8	chr2:96828200-96850000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:96829800-96833800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:96830200-96833200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:96830200-96833200	Weak transcription	HSMM	muscle
12	chr2:96830200-96833200	Weak transcription	HSMMtube	muscle
13	chr2:96830600-96831400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:96830600-96831400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:96830600-96831400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:96830600-96831800	Enhancers	Thymus	Thymus
17	chr2:96830600-96833400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:96830600-96833800	Weak transcription	NH-A	brain
19	chr2:96830600-96834000	Enhancers	Fetal Thymus	thymus
20	chr2:96830600-96850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:96830800-96832000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:96830800-96833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:96831000-96831600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:96831000-96831600	Enhancers	GM12878-XiMat	blood
25	chr2:96831000-96833400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:96831000-96833400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:96831000-96837600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:96831000-96840000	Weak transcription	Spleen	Spleen
29	chr2:96831200-96832200	Weak transcription	Primary T cells from cord blood	blood
30	chr2:96831200-96833600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:96831200-96833600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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