Variant report

Variant	rs2938340
Chromosome Location	chr1:114577595-114577596
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114573784..114577041-chr1:114577163..114579413,3	MCF-7	breast:
2	chr1:114577056..114579380-chr1:114582977..114584723,3	MCF-7	breast:
3	chr1:114543887..114546791-chr1:114577396..114579805,2	MCF-7	breast:
4	chr1:114524538..114527431-chr1:114576171..114578316,2	MCF-7	breast:
5	chr1:114569420..114571718-chr1:114573610..114578040,4	MCF-7	breast:
6	chr1:114575048..114578122-chr1:114756495..114758654,3	MCF-7	breast:
7	chr1:114572795..114577655-chr1:114580622..114587867,10	MCF-7	breast:
8	chr1:114575470..114578189-chr1:114589215..114591996,2	MCF-7	breast:
9	chr1:114575353..114578271-chr1:114615891..114617470,2	MCF-7	breast:
10	chr1:114520498..114523229-chr1:114575695..114578071,3	MCF-7	breast:
11	chr1:114574403..114579108-chr1:114596233..114599527,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116774	Chromatin interaction
ENSG00000270780	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10776776	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776777	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102721	1.00[ASN][1000 genomes]
rs11102722	1.00[ASN][1000 genomes]
rs1330700	1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs1394075	0.98[ASN][1000 genomes]
rs1587773	1.00[ASN][1000 genomes]
rs1604781	0.98[ASN][1000 genomes]
rs1910486	0.98[ASN][1000 genomes]
rs2938317	1.00[ASN][1000 genomes]
rs2938321	1.00[ASN][1000 genomes]
rs2938324	1.00[ASN][1000 genomes]
rs2938325	1.00[ASN][1000 genomes]
rs2938334	0.98[ASN][1000 genomes]
rs2938335	0.98[ASN][1000 genomes]
rs2938336	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938337	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938338	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938339	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2938341	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938342	0.98[ASN][1000 genomes]
rs2938343	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938344	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938345	0.98[ASN][1000 genomes]
rs2938349	0.95[ASN][1000 genomes]
rs2938350	0.95[ASN][1000 genomes]
rs2938351	0.98[ASN][1000 genomes]
rs2938353	0.83[ASN][1000 genomes]
rs3006985	0.88[ASN][1000 genomes]
rs3006986	0.88[ASN][1000 genomes]
rs3006991	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3006992	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006993	0.93[ASN][1000 genomes]
rs3006994	0.98[ASN][1000 genomes]
rs3006995	0.98[ASN][1000 genomes]
rs3006997	0.98[ASN][1000 genomes]
rs3007004	0.98[ASN][1000 genomes]
rs3007005	0.98[ASN][1000 genomes]
rs3007007	0.98[ASN][1000 genomes]
rs3007010	0.88[ASN][1000 genomes]
rs3007013	0.83[ASN][1000 genomes]
rs514647	0.83[ASN][1000 genomes]
rs529171	0.83[ASN][1000 genomes]
rs548040	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2754686	chr1:114531958-114602958	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2938340	TSPAN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114575000-114577600	Enhancers	HMEC	breast
2	chr1:114575000-114577800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr1:114575000-114578000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:114575000-114578400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:114575000-114578400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:114575200-114578400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:114575400-114577600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr1:114575800-114577800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:114576000-114577600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:114576000-114577800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:114576000-114579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:114576000-114580200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:114576000-114582800	Weak transcription	HSMMtube	muscle
14	chr1:114576000-114583400	Weak transcription	Lung	lung
15	chr1:114576400-114577600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:114576400-114579000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:114576600-114580400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:114576600-114582800	Weak transcription	Fetal Intestine Large	intestine
19	chr1:114576800-114578400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:114576800-114578800	Weak transcription	Fetal Intestine Small	intestine
21	chr1:114577000-114578200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:114577000-114580800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:114577200-114577600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:114577200-114578000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr1:114577200-114580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:114577200-114583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:114577400-114577600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:114577400-114577800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:114577400-114578800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:114577400-114580800	Weak transcription	NHEK	skin
31	chr1:114577400-114582000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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