Variant report

Variant	rs9750439
Chromosome Location	chr2:173079831-173079832
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	chr2:173078822..173080998-chr2:173095449..173097049,2	MCF-7	breast:
2	chr2:173074149..173078197-chr2:173078477..173081943,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10803868	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930527	0.83[ASN][1000 genomes]
rs10930528	0.84[ASN][1000 genomes]
rs10930529	0.84[ASN][1000 genomes]
rs10930530	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930531	0.87[ASN][1000 genomes]
rs10930532	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930533	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930534	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684103	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476259	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614495	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614868	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617862	0.88[ASN][1000 genomes]
rs12692997	1.00[EUR][1000 genomes]
rs12990778	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991095	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12995943	0.85[ASN][1000 genomes]
rs13019357	0.98[ASN][1000 genomes]
rs13034707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430020	0.88[EUR][1000 genomes]
rs1542676	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812500	0.95[ASN][1000 genomes]
rs1906181	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357320	0.89[ASN][1000 genomes]
rs2884154	0.88[ASN][1000 genomes]
rs4467239	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4524096	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4571029	0.98[ASN][1000 genomes]
rs4583429	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972710	0.84[ASN][1000 genomes]
rs4972711	0.94[ASN][1000 genomes]
rs4972712	0.94[ASN][1000 genomes]
rs4972713	0.85[ASN][1000 genomes]
rs4972715	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972716	0.87[ASN][1000 genomes]
rs4972717	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972718	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972719	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972723	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972728	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55919266	0.98[ASN][1000 genomes]
rs62168965	0.94[ASN][1000 genomes]
rs6433336	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433337	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433340	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6705155	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708636	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714712	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717806	0.87[ASN][1000 genomes]
rs6743328	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747259	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747365	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751574	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7575468	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963307	0.88[ASN][1000 genomes]
rs963308	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875413	chr2:173009413-173097343	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv3033	chr2:173063284-173108586	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173072600-173084200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:173073400-173080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:173074000-173080400	Weak transcription	Right Atrium	heart
4	chr2:173074400-173084600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:173076200-173084000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:173076800-173080200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:173077400-173081400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:173077400-173082600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:173077600-173087200	Weak transcription	Thymus	Thymus
10	chr2:173078000-173082200	Enhancers	HMEC	breast
11	chr2:173078200-173080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:173078200-173081800	Weak transcription	Fetal Thymus	thymus
13	chr2:173078200-173082200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:173078400-173080200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:173078400-173081600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:173078600-173080000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:173078600-173082200	Enhancers	NHEK	skin
18	chr2:173078600-173083400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:173078800-173082200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:173078800-173082200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:173079000-173080000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:173079000-173080000	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:173079000-173080600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:173079200-173080400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:173079400-173081400	Weak transcription	Aorta	Aorta
26	chr2:173079800-173080000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:173079800-173080400	Enhancers	Brain Germinal Matrix	brain
28	chr2:173079800-173080600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:173079800-173080600	Enhancers	Placenta	Placenta
30	chr2:173079800-173081400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:173079800-173081600	Enhancers	Brain Anterior Caudate	brain
32	chr2:173079800-173081600	Bivalent Enhancer	Fetal Brain Male	brain
33	chr2:173079800-173082000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:173079800-173092000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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