Variant report

Variant	rs12950438
Chromosome Location	chr17:59846353-59846354
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	chr17:59724447..59726120-chr17:59845901..59847755,2	MCF-7	breast:
2	chr17:59805564..59807713-chr17:59845299..59848078,3	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1015771	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515211	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11651510	0.86[EUR][1000 genomes]
rs11653175	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11657480	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11658539	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11871753	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451862	0.86[EUR][1000 genomes]
rs12453293	0.87[EUR][1000 genomes]
rs12453966	0.87[EUR][1000 genomes]
rs12935923	0.83[ASN][1000 genomes]
rs12937232	0.92[EUR][1000 genomes]
rs12948762	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12949659	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468577	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1978244	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990337	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1990338	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024188	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109252	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109254	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109255	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2159450	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2191247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2191249	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2378884	0.87[EUR][1000 genomes]
rs2378902	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378905	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2378906	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28571892	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2890021	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36031690	0.90[EUR][1000 genomes]
rs4309463	0.92[EUR][1000 genomes]
rs4343344	0.92[EUR][1000 genomes]
rs4580256	0.87[EUR][1000 genomes]
rs4968447	0.92[EUR][1000 genomes]
rs4988351	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57099937	0.87[EUR][1000 genomes]
rs57393813	0.87[EUR][1000 genomes]
rs62068837	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6504068	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504070	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504071	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504072	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717961	0.87[EUR][1000 genomes]
rs717962	0.86[EUR][1000 genomes]
rs7207074	0.87[EUR][1000 genomes]
rs7207881	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212172	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212423	0.92[EUR][1000 genomes]
rs7213329	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7213470	0.92[EUR][1000 genomes]
rs7213587	0.92[EUR][1000 genomes]
rs7213759	0.87[EUR][1000 genomes]
rs7214510	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7214884	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215784	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7216011	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216756	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7216824	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7217206	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7217292	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7220688	0.87[EUR][1000 genomes]
rs7220719	0.90[EUR][1000 genomes]
rs7222799	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074949	0.90[EUR][1000 genomes]
rs8075370	0.92[EUR][1000 genomes]
rs8075397	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8077088	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078977	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8182296	0.87[EUR][1000 genomes]
rs9807012	0.82[EUR][1000 genomes]
rs9889452	0.83[ASN][1000 genomes]
rs9895987	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9897121	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9897450	0.92[EUR][1000 genomes]
rs9897928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9900559	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9902995	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9904292	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9904294	0.92[EUR][1000 genomes]
rs9905870	0.89[EUR][1000 genomes]
rs9906313	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907299	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs991378	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
2	chr17:59804200-59847400	Weak transcription	K562	blood
3	chr17:59814000-59849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:59819400-59848200	Weak transcription	Primary B cells from cord blood	blood
6	chr17:59820000-59846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:59820400-59877200	Weak transcription	NH-A	brain
8	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
9	chr17:59827400-59847400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr17:59832200-59848400	Weak transcription	HepG2	liver
11	chr17:59835800-59848400	Weak transcription	Hela-S3	cervix
12	chr17:59839600-59847000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:59839800-59846400	Weak transcription	Fetal Muscle Leg	muscle
14	chr17:59839800-59849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:59840200-59847400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:59840200-59848200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:59840600-59848000	Weak transcription	Fetal Lung	lung
18	chr17:59840600-59848400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:59840800-59847200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:59840800-59848600	Weak transcription	Fetal Thymus	thymus
21	chr17:59841000-59847400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:59841600-59848000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:59841600-59856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:59842000-59847200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:59842000-59848200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr17:59842600-59846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:59842600-59847400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:59842600-59848200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:59844000-59851600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:59844000-59882600	Weak transcription	NHLF	lung
31	chr17:59844600-59847000	Weak transcription	NHEK	skin
32	chr17:59844600-59882600	Weak transcription	HMEC	breast
33	chr17:59844800-59847200	Weak transcription	NHDF-Ad	bronchial
34	chr17:59844800-59848000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:59845000-59846400	Weak transcription	Osteobl	bone
36	chr17:59845000-59853200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:59845200-59847200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:59845200-59848200	Strong transcription	Dnd41	blood
39	chr17:59845400-59846600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr17:59845400-59847400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr17:59845600-59848000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:59845600-59850000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:59845800-59847800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr17:59845800-59848000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr17:59845800-59849000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:59846000-59846400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:59846000-59847400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:59846000-59847600	Strong transcription	A549	lung
49	chr17:59846000-59850000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:59846200-59846800	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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