Variant report

Variant	rs17713143
Chromosome Location	chr7:39504842-39504843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38836355..38837155-chr7:39503792..39504917,3	MCF-7	breast:
2	chr7:38836202..38837177-chr7:39504337..39505154,4	K562	blood:
3	chr7:38836232..38836866-chr7:39504695..39505205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006715	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12111665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12112344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17171576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17171578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17713095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17713107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17769981	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17769987	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2052018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2052019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2073539	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237386	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237394	0.81[ASN][1000 genomes]
rs2237397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2237399	0.81[ASN][1000 genomes]
rs2282915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2299134	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs3800850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3819416	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388309	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73388311	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs980392	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv966782	chr7:39454992-39581886	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39502600-39508000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:39503400-39505400	Enhancers	Primary hematopoietic stem cells	blood
3	chr7:39504000-39505000	Enhancers	Fetal Muscle Leg	muscle
4	chr7:39504000-39505200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:39504000-39505800	Enhancers	Fetal Thymus	thymus
6	chr7:39504200-39505200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:39504200-39508400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:39504400-39505000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr7:39504400-39505000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:39504400-39505000	Active TSS	Right Ventricle	heart
11	chr7:39504400-39505200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:39504400-39505200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr7:39504600-39505000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr7:39504600-39505000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:39504600-39505000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr7:39504600-39507800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:39504800-39505000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:39504800-39505000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:39504800-39505000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr7:39504800-39505000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:39504800-39505000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:39504800-39505000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:39504800-39505000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:39504800-39505000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:39504800-39505000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:39504800-39505000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
27	chr7:39504800-39505000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:39504800-39505000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:39504800-39505000	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr7:39504800-39505000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr7:39504800-39505000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
32	chr7:39504800-39505000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr7:39504800-39505000	Enhancers	Fetal Brain Female	brain
34	chr7:39504800-39505000	Enhancers	Fetal Heart	heart
35	chr7:39504800-39505000	Enhancers	Fetal Kidney	kidney
36	chr7:39504800-39505000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr7:39504800-39505000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:39504800-39505000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr7:39504800-39505000	Flanking Active TSS	Hela-S3	cervix
40	chr7:39504800-39505000	Flanking Active TSS	HSMM	muscle
41	chr7:39504800-39505000	Flanking Active TSS	K562	blood
42	chr7:39504800-39505000	Enhancers	NH-A	brain
43	chr7:39504800-39505000	Flanking Active TSS	Osteobl	bone
44	chr7:39504800-39505200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr7:39504800-39505200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr7:39504800-39505200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:39504800-39505200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:39504800-39505200	Flanking Active TSS	Liver	Liver
49	chr7:39504800-39505200	Enhancers	Fetal Lung	lung
50	chr7:39504800-39505200	Enhancers	Thymus	Thymus

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