Variant report

Variant	rs9889938
Chromosome Location	chr17:19891969-19891970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11204422	1.00[JPT][hapmap]
rs11867585	0.92[JPT][hapmap]
rs11870381	1.00[JPT][hapmap]
rs12451841	1.00[JPT][hapmap]
rs12942179	0.92[JPT][hapmap]
rs12947713	0.91[JPT][hapmap]
rs1638526	0.90[JPT][hapmap]
rs16960545	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs16960602	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17686798	1.00[JPT][hapmap]
rs17759959	0.91[JPT][hapmap]
rs2072337	0.82[JPT][hapmap]
rs28424266	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28581607	1.00[EUR][1000 genomes]
rs28653561	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28767032	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28830504	0.81[AFR][1000 genomes]
rs28865331	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3909257	0.81[AFR][1000 genomes]
rs4141185	0.90[JPT][hapmap]
rs4570919	0.91[JPT][hapmap]
rs4924808	1.00[JPT][hapmap]
rs4925075	1.00[JPT][hapmap]
rs4925082	1.00[JPT][hapmap]
rs4925088	0.82[JPT][hapmap]
rs6587207	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6587208	0.81[AFR][1000 genomes]
rs7207459	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7207702	0.81[AFR][1000 genomes]
rs7209653	0.90[JPT][hapmap]
rs7210076	0.81[AFR][1000 genomes]
rs7210751	0.81[AFR][1000 genomes]
rs7214107	0.81[AFR][1000 genomes]
rs7215639	1.00[EUR][1000 genomes]
rs7215769	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7215803	1.00[JPT][hapmap]
rs7217387	0.81[AFR][1000 genomes]
rs7217862	0.81[AFR][1000 genomes]
rs7217868	0.81[AFR][1000 genomes]
rs7217928	1.00[EUR][1000 genomes]
rs7218251	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7219153	0.81[AFR][1000 genomes]
rs7219487	0.81[AFR][1000 genomes]
rs7220490	0.81[AFR][1000 genomes]
rs7221669	0.81[AFR][1000 genomes]
rs7223323	0.81[AFR][1000 genomes]
rs7224419	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7224567	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7224713	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7224875	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8065122	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8068015	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8068484	0.91[JPT][hapmap]
rs8068488	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071670	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8075343	0.91[JPT][hapmap]
rs8079093	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8079487	1.00[EUR][1000 genomes]
rs8080190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs888424	1.00[JPT][hapmap]
rs9892175	0.81[AFR][1000 genomes]
rs9892271	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9893185	0.81[AFR][1000 genomes]
rs9893296	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9894666	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9895556	0.82[AFR][1000 genomes]
rs9896010	0.81[AFR][1000 genomes]
rs9896387	0.81[AFR][1000 genomes]
rs9896499	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9896633	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9896641	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9897430	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9897607	0.81[AFR][1000 genomes]
rs9897653	0.92[JPT][hapmap]
rs9898618	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900441	0.81[AFR][1000 genomes]
rs9900510	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9901862	0.81[AFR][1000 genomes]
rs9902663	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9903631	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904059	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9908415	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9909242	0.81[AFR][1000 genomes]
rs9909544	0.81[AFR][1000 genomes]
rs9911408	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9912184	1.00[EUR][1000 genomes]
rs9912648	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912657	0.81[AFR][1000 genomes]
rs9913858	1.00[EUR][1000 genomes]
rs9914328	0.81[AFR][1000 genomes]
rs9914429	0.81[AFR][1000 genomes]
rs9915039	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9915413	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9944451	0.92[JPT][hapmap]

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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19889400-19892200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:19890400-19892000	Enhancers	K562	blood
3	chr17:19890600-19899800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr17:19890800-19896400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:19890800-19899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:19890800-19899800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:19890800-19899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:19891000-19894000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:19891000-19894200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:19891400-19894200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:19891400-19894400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:19891400-19894800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:19891400-19896400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:19891600-19899800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr17:19891800-19894800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:19891800-19896400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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