Variant report

Variant	rs9924964
Chromosome Location	chr16:72085561-72085562
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72041448..72043956-chr16:72084241..72086257,2	MCF-7	breast:
2	chr16:72079240..72082206-chr16:72084607..72086116,2	K562	blood:

Variant related genes	Relation type
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10048144	0.81[AMR][1000 genomes]
rs10400963	0.85[JPT][hapmap]
rs10492813	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs10492814	1.00[YRI][hapmap]
rs1050361	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1050363	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs10852511	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11075924	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs12162087	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443622	0.92[ASN][1000 genomes]
rs12446480	0.88[ASN][1000 genomes]
rs12449073	0.85[JPT][hapmap];0.83[YRI][hapmap]
rs12917999	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12924413	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12928365	0.81[EUR][1000 genomes]
rs12930205	0.84[ASN][1000 genomes]
rs12930702	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12932845	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12935266	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1465457	0.94[YRI][hapmap]
rs16973716	0.89[JPT][hapmap]
rs2000999	0.84[JPT][hapmap]
rs2070937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2072141	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2074626	0.84[JPT][hapmap]
rs2081222	0.88[ASN][1000 genomes]
rs2081223	0.85[ASN][1000 genomes]
rs217181	1.00[YRI][hapmap]
rs2236765	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241411	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241412	0.86[YRI][hapmap]
rs2287998	0.85[ASN][1000 genomes]
rs2287999	0.86[ASN][1000 genomes]
rs2288000	0.84[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2288001	0.86[ASN][1000 genomes]
rs2288002	0.84[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2303285	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs251033	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2550035	0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2550038	0.80[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2550868	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2550869	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2550870	0.92[ASN][1000 genomes]
rs2550876	0.90[ASN][1000 genomes]
rs2854956	0.81[JPT][hapmap]
rs3764311	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs3764314	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs3812984	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3812986	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs3812987	0.80[JPT][hapmap]
rs3844425	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs3852781	0.85[JPT][hapmap];0.94[YRI][hapmap]
rs3852782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3852784	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs3890860	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3909541	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs3909542	0.81[EUR][1000 genomes]
rs4238964	0.84[JPT][hapmap]
rs4788458	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788461	0.88[EUR][1000 genomes]
rs4788609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs4788610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs56139130	0.96[ASN][1000 genomes]
rs6499557	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499562	0.89[JPT][hapmap]
rs6499563	0.87[EUR][1000 genomes]
rs7185840	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7186155	0.86[EUR][1000 genomes]
rs7188962	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7189115	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7189591	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7190994	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7190995	0.81[JPT][hapmap];0.83[YRI][hapmap]
rs7191127	0.81[JPT][hapmap];0.83[YRI][hapmap]
rs7199261	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7200003	0.83[EUR][1000 genomes]
rs7200854	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7201643	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7201866	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202268	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203426	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203821	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7350838	0.87[ASN][1000 genomes]
rs7940	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8044868	0.89[JPT][hapmap]
rs8051882	0.86[YRI][hapmap]
rs8052338	0.85[JPT][hapmap]
rs8052408	0.89[JPT][hapmap]
rs8053907	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8059437	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8060770	0.89[EUR][1000 genomes]
rs8062041	0.85[JPT][hapmap]
rs8062895	0.92[YRI][hapmap]
rs8182213	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9926156	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs9926927	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9927526	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs9928157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9930890	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9932951	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9938382	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv906895	chr16:72083318-72106756	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
10	nsv906896	chr16:72083318-72114002	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
11	nsv827729	chr16:72083719-72110251	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
12	nsv9456	chr16:72084761-72118322	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9924964	DHX38	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
3	chr16:72076200-72098200	Weak transcription	Fetal Heart	heart
4	chr16:72076600-72092400	Weak transcription	Left Ventricle	heart
5	chr16:72077000-72107400	Weak transcription	Right Ventricle	heart
6	chr16:72077400-72102400	Weak transcription	Brain Substantia Nigra	brain
7	chr16:72077400-72107400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr16:72077600-72107400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:72078000-72090000	Weak transcription	Gastric	stomach
10	chr16:72078000-72100800	Weak transcription	Brain Hippocampus Middle	brain
11	chr16:72078000-72103200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:72078200-72095600	Weak transcription	Brain Anterior Caudate	brain
13	chr16:72078200-72105200	Weak transcription	Brain Angular Gyrus	brain
14	chr16:72078400-72098400	Weak transcription	Primary T cells from cord blood	blood
15	chr16:72078400-72105400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr16:72078400-72108000	Weak transcription	Aorta	Aorta
17	chr16:72082800-72087800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr16:72084000-72087800	Enhancers	HepG2	liver
19	chr16:72084200-72089400	Weak transcription	Primary B cells from cord blood	blood
20	chr16:72084200-72090200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr16:72084400-72087000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr16:72084600-72085800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:72084600-72087200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr16:72084600-72106800	Weak transcription	Psoas Muscle	Psoas
25	chr16:72084800-72087800	Enhancers	Liver	Liver
26	chr16:72084800-72098200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr16:72085000-72086000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr16:72085000-72089800	Weak transcription	Lung	lung
29	chr16:72085200-72085600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:72085400-72085800	Weak transcription	Adipose Nuclei	Adipose
31	chr16:72085400-72086000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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