Variant report

Variant	rs1030407
Chromosome Location	chr2:64552357-64552358
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64364705..64366411-chr2:64549712..64552538,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10187442	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1030410	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125996	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673882	0.84[ASN][1000 genomes]
rs11682772	0.84[ASN][1000 genomes]
rs11683866	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs11883600	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365474	0.82[ASN][1000 genomes]
rs1365475	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1426698	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs1426699	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs1426701	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs1426702	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs1426703	0.80[ASN][1000 genomes]
rs1426712	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1974976	0.82[ASN][1000 genomes]
rs2059630	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs2263647	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278184	0.86[ASN][1000 genomes]
rs2555423	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2555448	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4485554	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4597511	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546064	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546065	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6714101	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748843	0.81[ASN][1000 genomes]
rs6758664	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561343	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565077	0.85[ASN][1000 genomes]
rs7585084	0.84[ASN][1000 genomes]
rs7601758	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7601803	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890478	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919122	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs919123	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919124	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919125	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919126	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs919127	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930020	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
2	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
4	chr2:64549200-64555800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:64549400-64553400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr2:64549400-64555200	Weak transcription	Placenta	Placenta
7	chr2:64549600-64554400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:64549800-64555000	Weak transcription	Fetal Lung	lung
9	chr2:64550200-64553400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:64550400-64552600	Weak transcription	Fetal Thymus	thymus
11	chr2:64550400-64554400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:64550600-64553000	Enhancers	Primary T cells from cord blood	blood
13	chr2:64550600-64554600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:64550800-64552800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:64550800-64554400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:64551000-64552600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:64551000-64553000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:64551200-64554200	Weak transcription	Esophagus	oesophagus
19	chr2:64551600-64552600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:64551800-64554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:64552000-64552800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:64552000-64552800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:64552000-64553000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:64552000-64553000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr2:64552000-64554600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:64552000-64554600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:64552000-64554600	Enhancers	Thymus	Thymus
28	chr2:64552000-64555800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:64552200-64552600	Enhancers	GM12878-XiMat	blood
30	chr2:64552200-64552800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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