Variant report

Variant	rs6489237
Chromosome Location	chr12:123208929-123208930
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	chr12:123201536..123203616-chr12:123208338..123210644,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10444445	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10773474	0.82[ASN][1000 genomes]
rs10773515	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773516	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10847574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059504	0.89[ASN][1000 genomes]
rs11059507	0.89[ASN][1000 genomes]
rs11059583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2649912	0.86[ASN][1000 genomes]
rs35173057	0.92[ASN][1000 genomes]
rs55776099	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61955029	0.89[ASN][1000 genomes]
rs7131790	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131791	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307192	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313367	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	esv13329	chr12:123178106-123210671	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	esv3348872	chr12:123192296-123213461	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123201200-123214600	Weak transcription	Spleen	Spleen
2	chr12:123201400-123209400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:123201400-123210000	Weak transcription	Primary B cells from cord blood	blood
4	chr12:123205200-123214600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:123205800-123209000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:123205800-123209800	Weak transcription	Hela-S3	cervix
7	chr12:123205800-123210400	Weak transcription	Placenta	Placenta
8	chr12:123205800-123210400	Weak transcription	NH-A	brain
9	chr12:123207000-123209400	Weak transcription	NHEK	skin
10	chr12:123207000-123209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:123207000-123209600	Weak transcription	HUVEC	blood vessel
12	chr12:123207000-123210000	Weak transcription	Fetal Intestine Small	intestine
13	chr12:123207400-123209600	Weak transcription	HMEC	breast
14	chr12:123207400-123214200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:123207800-123209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:123207800-123209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:123207800-123210000	Weak transcription	Fetal Intestine Large	intestine
18	chr12:123207800-123214800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:123208000-123209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:123208000-123209400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:123208000-123209600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:123208000-123209600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:123208200-123209600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:123208200-123209600	Weak transcription	HepG2	liver
25	chr12:123208200-123209600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:123208200-123209800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:123208200-123210200	Weak transcription	Adipose Nuclei	Adipose
28	chr12:123208200-123214200	Weak transcription	Fetal Thymus	thymus
29	chr12:123208200-123215200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr12:123208200-123217000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:123208400-123209200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:123208400-123209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:123208800-123209600	Enhancers	GM12878-XiMat	blood

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