Variant report

Variant	rs12993424
Chromosome Location	chr2:99365589-99365590
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	chr2:99363918..99365909-chr2:99377187..99378693,2	MCF-7	breast:
2	chr2:99358144..99360845-chr2:99364555..99366061,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1016124	0.94[ASN][1000 genomes]
rs10166044	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10174321	0.83[ASN][1000 genomes]
rs10177696	0.89[ASN][1000 genomes]
rs10194177	0.89[ASN][1000 genomes]
rs10200288	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210711	0.81[ASN][1000 genomes]
rs10496332	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs11123747	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11123749	0.94[ASN][1000 genomes]
rs11123751	0.95[CHB][hapmap]
rs11885883	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs12471383	0.94[ASN][1000 genomes]
rs12477450	0.95[CHB][hapmap]
rs12615301	0.96[ASN][1000 genomes]
rs13391483	0.96[ASN][1000 genomes]
rs1514916	0.89[ASN][1000 genomes]
rs1517681	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913621	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2013983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28783173	0.94[ASN][1000 genomes]
rs34521960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35477458	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41445250	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4851150	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4851153	0.85[ASN][1000 genomes]
rs4851154	0.96[ASN][1000 genomes]
rs58666702	0.89[ASN][1000 genomes]
rs6712597	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6716514	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6740656	0.87[ASN][1000 genomes]
rs6743770	0.81[EUR][1000 genomes]
rs7420869	0.89[ASN][1000 genomes]
rs7558236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7581128	0.80[CHB][hapmap]
rs7599792	0.93[ASN][1000 genomes]
rs885036	0.81[JPT][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv1002315	chr2:99361475-99368975	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
2	chr2:99359600-99367200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:99359600-99374000	Weak transcription	Aorta	Aorta
4	chr2:99361400-99365600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:99361400-99374000	Weak transcription	Pancreas	Pancrea
6	chr2:99362400-99372800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:99363400-99366000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:99364000-99365800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:99364200-99365800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:99364200-99366000	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:99364200-99366000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:99364200-99366600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:99364200-99367200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:99364400-99365800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:99364400-99365800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:99364400-99365800	Flanking Active TSS	GM12878-XiMat	blood
17	chr2:99364400-99366000	Enhancers	HMEC	breast
18	chr2:99364600-99365800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:99364800-99365800	Weak transcription	Dnd41	blood
20	chr2:99364800-99367000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:99364800-99371200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:99365000-99365800	Enhancers	Primary B cells from cord blood	blood
23	chr2:99365000-99368200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:99365200-99365600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:99365200-99365600	Weak transcription	Fetal Thymus	thymus
26	chr2:99365200-99365600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr2:99365200-99372200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:99365400-99366000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:99365400-99366200	Enhancers	Fetal Lung	lung
30	chr2:99365400-99367200	Weak transcription	Placenta	Placenta
31	chr2:99365400-99371600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:99365400-99372400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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