Variant report

Variant	rs16890448
Chromosome Location	chr6:25350666-25350667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25348848..25351253-chr6:25357378..25359021,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11491476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965829	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11967836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16890454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56930318	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57899991	0.93[ASN][1000 genomes]
rs60384851	0.93[ASN][1000 genomes]
rs6456670	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6456671	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6456672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6456673	0.93[ASN][1000 genomes]
rs6456674	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6456675	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6456676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6456677	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6932311	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73399971	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7750545	0.80[AFR][1000 genomes]
rs7750609	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7770521	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9461142	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9461143	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461144	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467474	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9986335	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9986525	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9986604	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9986608	0.89[AFR][1000 genomes];0.93[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv275059	chr6:25346985-25351263	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv1792912	chr6:25349637-25354122	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
3	chr6:25337400-25357800	Weak transcription	NHEK	skin
4	chr6:25341000-25352800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
6	chr6:25342800-25351800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:25342800-25354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:25343000-25352600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:25343800-25354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:25346800-25351800	Weak transcription	Fetal Intestine Small	intestine
12	chr6:25346800-25352800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:25347000-25352400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:25347000-25354200	Weak transcription	Stomach Mucosa	stomach
16	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:25347200-25351600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:25349200-25359200	Weak transcription	Ovary	ovary
19	chr6:25349400-25351200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:25349600-25354200	Weak transcription	Aorta	Aorta
21	chr6:25350000-25350800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:25350200-25350800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:25350200-25350800	Enhancers	Lung	lung
24	chr6:25350400-25351200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:25350400-25355200	Enhancers	Fetal Lung	lung
26	chr6:25350600-25350800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:25350600-25350800	Enhancers	Fetal Thymus	thymus
28	chr6:25350600-25350800	Enhancers	Left Ventricle	heart
29	chr6:25350600-25351400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:25350600-25351400	Enhancers	Small Intestine	intestine
31	chr6:25350600-25351400	Enhancers	Stomach Smooth Muscle	stomach
32	chr6:25350600-25351800	Enhancers	HSMMtube	muscle
33	chr6:25350600-25352600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:25350600-25356000	Enhancers	Fetal Intestine Large	intestine

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