Variant report

Variant	rs2938342
Chromosome Location	chr1:114580510-114580511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114565136..114566738-chr1:114579035..114581815,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10776776	0.98[ASN][1000 genomes]
rs10776777	0.98[ASN][1000 genomes]
rs10858028	0.85[EUR][1000 genomes]
rs11102721	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102722	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330700	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1394075	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1587773	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604781	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910486	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938317	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938321	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938324	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938325	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938334	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938335	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938336	0.98[ASN][1000 genomes]
rs2938337	0.98[ASN][1000 genomes]
rs2938338	0.98[ASN][1000 genomes]
rs2938339	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938340	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2938341	0.98[ASN][1000 genomes]
rs2938343	0.93[ASN][1000 genomes]
rs2938344	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2938345	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938349	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938350	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938351	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938353	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3006985	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3006986	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3006991	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006992	0.98[ASN][1000 genomes]
rs3006993	0.91[ASN][1000 genomes]
rs3006994	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006995	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006997	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007004	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007005	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007007	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007010	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3007012	0.90[EUR][1000 genomes]
rs3007013	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4240537	0.86[EUR][1000 genomes]
rs514647	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs529171	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548040	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114576000-114582800	Weak transcription	HSMMtube	muscle
2	chr1:114576000-114583400	Weak transcription	Lung	lung
3	chr1:114576600-114582800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:114577000-114580800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:114577200-114580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:114577200-114583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:114577400-114580800	Weak transcription	NHEK	skin
8	chr1:114577400-114582000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:114577600-114580800	Weak transcription	HMEC	breast
10	chr1:114577800-114583000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:114578000-114582200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:114578200-114583000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:114578600-114580800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:114578600-114582400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:114579000-114583800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:114579200-114580800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:114579400-114580800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:114579400-114582000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:114579600-114581600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:114579600-114581800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:114579800-114581600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:114580200-114580600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:114580200-114581200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:114580200-114581200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:114580200-114581200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:114580200-114581200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:114580200-114581400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:114580200-114581800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:114580200-114582000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:114580200-114583000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:114580400-114581200	Enhancers	Skeletal Muscle Male	skeletal muscle

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