Variant report

Variant	rs17152400
Chromosome Location	chr10:6281215-6281216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6279091..6282826-chr10:6339063..6342558,5	MCF-7	breast:
2	chr10:6253749..6256671-chr10:6278525..6281459,3	MCF-7	breast:
3	chr10:6243300..6247795-chr10:6278490..6283454,9	MCF-7	breast:
4	chr10:6244951..6247440-chr10:6279322..6281493,5	MCF-7	breast:
5	chr10:6267486..6269142-chr10:6279935..6282676,2	MCF-7	breast:
6	chr10:6275845..6278473-chr10:6279754..6281558,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12244701	0.85[AMR][1000 genomes]
rs1539234	0.92[YRI][hapmap]
rs17152229	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17152396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35929982	0.93[ASN][1000 genomes]
rs56046905	0.97[AFR][1000 genomes]
rs57879330	0.83[ASN][1000 genomes]
rs59400494	0.83[AFR][1000 genomes]
rs7074366	1.00[ASN][1000 genomes]
rs7088179	1.00[ASN][1000 genomes]
rs74112209	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74112210	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74112211	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74112213	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv525622	chr10:6251252-6281215	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6270600-6288600	Weak transcription	Fetal Kidney	kidney
2	chr10:6273600-6287800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:6275800-6291000	Weak transcription	Psoas Muscle	Psoas
4	chr10:6276200-6283000	Weak transcription	Primary B cells from cord blood	blood
5	chr10:6276400-6282600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:6276400-6286200	Weak transcription	Colonic Mucosa	Colon
7	chr10:6276400-6288000	Weak transcription	Brain Angular Gyrus	brain
8	chr10:6276400-6288800	Weak transcription	Right Ventricle	heart
9	chr10:6276600-6284000	Weak transcription	Fetal Lung	lung
10	chr10:6276600-6286800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:6276600-6288800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:6276800-6303800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:6277000-6284000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:6278400-6281600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr10:6278600-6283400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:6278600-6285400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:6278600-6287400	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:6278600-6288800	Weak transcription	Aorta	Aorta
19	chr10:6278600-6297600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:6278800-6286400	Weak transcription	Brain Substantia Nigra	brain
21	chr10:6278800-6288600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:6278800-6288800	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:6278800-6289400	Weak transcription	Small Intestine	intestine
24	chr10:6278800-6295400	Weak transcription	Pancreas	Pancrea
25	chr10:6278800-6312400	Weak transcription	Thymus	Thymus
26	chr10:6279000-6290200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:6279000-6291600	Weak transcription	Fetal Intestine Small	intestine
28	chr10:6279200-6283400	Weak transcription	Fetal Stomach	stomach
29	chr10:6279200-6288800	Weak transcription	Brain Anterior Caudate	brain
30	chr10:6279200-6289400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:6279200-6289400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:6279200-6303400	Weak transcription	Primary T cells from cord blood	blood
33	chr10:6279400-6281600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:6279400-6285600	Weak transcription	Gastric	stomach
35	chr10:6279400-6286000	Weak transcription	Esophagus	oesophagus
36	chr10:6279400-6288600	Weak transcription	Ovary	ovary
37	chr10:6279400-6289000	Weak transcription	Brain Germinal Matrix	brain
38	chr10:6279800-6284400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:6280600-6281600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:6280600-6281600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:6280600-6281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:6280600-6281800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr10:6280600-6282000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr10:6280600-6282000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr10:6280800-6281600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr10:6280800-6281600	Enhancers	Rectal Smooth Muscle	rectum
47	chr10:6280800-6281800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr10:6280800-6282000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:6280800-6282000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:6281000-6281400	Enhancers	HUES6 Cell Line	embryonic stem cell

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