Variant report

Variant	rs10939649
Chromosome Location	chr4:16034589-16034590
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	chr4:16033674..16036542-chr4:16143122..16145633,2	MCF-7	breast:
2	chr4:16026900..16029773-chr4:16034427..16036480,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11730129	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732612	0.81[CEU][hapmap]
rs13133886	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850507	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2292804	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677795	0.86[CHB][hapmap]
rs884718	0.87[CHB][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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10939649	PROM1	cis	Artery Aorta	GTEx
rs10939649	PROM1	cis	Artery Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16010800-16038600	Weak transcription	Placenta	Placenta
2	chr4:16025600-16035600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:16025600-16045000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16025600-16050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:16025800-16036000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:16025800-16057600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:16026400-16066600	Weak transcription	Colonic Mucosa	Colon
8	chr4:16026400-16066600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:16027200-16039000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:16027600-16036000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:16030400-16036000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:16030400-16039000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:16030800-16035000	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:16031000-16034600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr4:16031200-16035200	Weak transcription	Liver	Liver
16	chr4:16031200-16035600	Weak transcription	Aorta	Aorta
17	chr4:16031200-16035800	Weak transcription	NHDF-Ad	bronchial
18	chr4:16031200-16040000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:16031600-16034600	Weak transcription	Hela-S3	cervix
20	chr4:16031600-16035800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:16031600-16036000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:16031600-16036000	Weak transcription	A549	lung
23	chr4:16031800-16035600	Weak transcription	HSMMtube	muscle
24	chr4:16032400-16036600	Enhancers	Fetal Brain Male	brain
25	chr4:16032800-16034600	Genic enhancers	Fetal Muscle Leg	muscle
26	chr4:16032800-16035000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:16032800-16035000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:16032800-16035200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:16032800-16039800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:16033000-16035000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:16033000-16035200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:16033000-16037600	Enhancers	HepG2	liver
33	chr4:16033000-16039800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:16033200-16034600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr4:16033200-16034600	Enhancers	Brain Anterior Caudate	brain
36	chr4:16033200-16034800	Enhancers	Adipose Nuclei	Adipose
37	chr4:16033200-16035000	Enhancers	HUVEC	blood vessel
38	chr4:16033200-16035200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:16033200-16035200	Enhancers	Brain Substantia Nigra	brain
40	chr4:16033200-16035400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr4:16033200-16039200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:16033200-16039600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr4:16033600-16035000	Enhancers	Fetal Brain Female	brain
44	chr4:16033600-16035200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr4:16033800-16034800	Enhancers	H9 Cell Line	embryonic stem cell
46	chr4:16033800-16035200	Enhancers	Brain Angular Gyrus	brain
47	chr4:16033800-16036400	Enhancers	NH-A	brain
48	chr4:16033800-16038400	Weak transcription	Primary B cells from cord blood	blood
49	chr4:16034000-16034600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:16034000-16034600	Flanking Active TSS	Brain Cingulate Gyrus	brain

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