Variant report

Variant	rs17748374
Chromosome Location	chr6:53678150-53678151
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	chr6:53588027..53590620-chr6:53675669..53678421,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10456165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10456673	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs10456674	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10948782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10948785	0.86[AMR][1000 genomes]
rs11962552	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11968082	0.81[ASN][1000 genomes]
rs11970064	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12192118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192689	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12195491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs12200971	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12201245	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12201913	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12202128	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12202762	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12204130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12206209	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211417	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12211478	0.81[ASN][1000 genomes]
rs12211680	0.86[JPT][hapmap]
rs12213392	0.86[JPT][hapmap]
rs12213577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12214863	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12216441	0.81[ASN][1000 genomes]
rs13205690	0.81[ASN][1000 genomes]
rs13211528	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1883632	0.82[LWK][hapmap]
rs34113003	0.82[AFR][1000 genomes]
rs35078422	0.81[ASN][1000 genomes]
rs35143842	0.81[ASN][1000 genomes]
rs35971619	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935663	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4373362	0.81[ASN][1000 genomes]
rs4389767	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4639324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55678884	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55931905	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6919015	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72941941	0.81[ASN][1000 genomes]
rs7739668	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7745930	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7762326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
4	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:53668800-53683800	Weak transcription	Ovary	ovary
6	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
12	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:53673000-53678400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:53673600-53682800	Weak transcription	Dnd41	blood
16	chr6:53673800-53678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:53674200-53678200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:53674800-53678400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53674800-53679600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
21	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
22	chr6:53675400-53679000	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
24	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr6:53675600-53678200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr6:53675600-53678800	Enhancers	Hela-S3	cervix
27	chr6:53676200-53678400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:53676200-53678600	Enhancers	Esophagus	oesophagus
29	chr6:53676200-53678800	Enhancers	Gastric	stomach
30	chr6:53676200-53679200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:53676200-53683600	Weak transcription	Left Ventricle	heart
32	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:53676400-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:53676400-53678400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:53676400-53679200	Weak transcription	Brain Angular Gyrus	brain
36	chr6:53676400-53679800	Weak transcription	Fetal Heart	heart
37	chr6:53676600-53679400	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:53676800-53678600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:53676800-53679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:53676800-53680000	Weak transcription	Pancreas	Pancrea
41	chr6:53676800-53680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:53676800-53680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
44	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:53677000-53678400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:53677000-53678400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:53677000-53678400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:53677000-53678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:53677000-53678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:53677000-53678600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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