Variant report

Variant	rs11864453
Chromosome Location	chr16:72050480-72050481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72047753..72049344-chr16:72049457..72051063,2	MCF-7	breast:
2	chr16:72049013..72051278-chr16:72125940..72127742,2	MCF-7	breast:
3	chr16:72049896..72052834-chr16:72059400..72062062,3	K562	blood:

Variant related genes	Relation type
ENSG00000140829	Chromatin interaction
ENSG00000102967	Chromatin interaction
ENSG00000140830	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10048111	0.80[ASN][1000 genomes]
rs1035559	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1035560	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10492813	0.87[GIH][hapmap]
rs10492814	0.87[GIH][hapmap]
rs1050362	0.84[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs11642993	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11648003	0.91[ASN][1000 genomes]
rs12325142	0.84[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs12708928	0.80[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs2072142	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs2074626	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs2074627	0.84[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs2240243	0.80[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs2241412	0.89[GIH][hapmap]
rs2278027	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303285	0.87[GIH][hapmap]
rs2550035	0.87[GIH][hapmap]
rs2854956	0.84[CEU][hapmap]
rs3213420	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213422	0.89[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764312	0.91[GIH][hapmap]
rs3764314	0.87[GIH][hapmap]
rs6680	0.87[GIH][hapmap]
rs7185215	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7185407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7186207	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7195958	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7201491	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8051239	0.85[ASN][1000 genomes]
rs8051882	0.91[GIH][hapmap]
rs8062041	0.82[CEU][hapmap]
rs9926927	0.87[GIH][hapmap]
rs9941087	0.80[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	esv1843253	chr16:72042428-72059149	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11864453	DHX38	cis	multi-tissue	Pritchard
rs11864453	HPR	cis	cerebellum	SCAN
rs11864453	DHODH	cis	Nerve Tibial	GTEx
rs11864453	DHX38	cis	lymphoblastoid	seeQTL
rs11864453	NRN1L	cis	parietal	SCAN
rs11864453	HP	cis	parietal	SCAN
rs11864453	DHODH	cis	parietal	SCAN
rs11864453	DHODH	cis	Esophagus Muscularis	GTEx
rs11864453	HPR	cis	parietal	SCAN
rs11864453	DHODH	cis	cerebellum	SCAN
rs11864453	DHODH	cis	Artery Tibial	GTEx
rs11864453	HP	cis	cerebellum	SCAN
rs11864453	DHX38	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043000-72063000	Weak transcription	Small Intestine	intestine
2	chr16:72043200-72051000	Weak transcription	Fetal Lung	lung
3	chr16:72043200-72051800	Weak transcription	Fetal Thymus	thymus
4	chr16:72043200-72052200	Weak transcription	Brain Angular Gyrus	brain
5	chr16:72043200-72053400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr16:72043200-72054000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr16:72043200-72054600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr16:72043200-72054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:72043200-72054800	Weak transcription	Pancreas	Pancrea
10	chr16:72043200-72055000	Weak transcription	Colon Smooth Muscle	Colon
11	chr16:72043200-72055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr16:72043200-72055200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr16:72043200-72056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:72043200-72056600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr16:72043200-72057400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:72043200-72057800	Weak transcription	NHDF-Ad	bronchial
17	chr16:72043200-72061200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr16:72043200-72062800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr16:72043200-72069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:72043200-72069800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr16:72043400-72051000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:72043600-72075200	Weak transcription	Fetal Brain Male	brain
23	chr16:72043800-72051200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:72043800-72056800	Weak transcription	HSMM	muscle
25	chr16:72044000-72054800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr16:72044000-72057400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr16:72045600-72053400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:72045600-72059400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:72045600-72060200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:72045600-72060400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:72045600-72060600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:72045600-72062200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:72045600-72062400	Strong transcription	Dnd41	blood
34	chr16:72045800-72052600	Strong transcription	Fetal Intestine Small	intestine
35	chr16:72045800-72060200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr16:72045800-72060400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr16:72045800-72060400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:72045800-72064200	Strong transcription	Fetal Stomach	stomach
39	chr16:72046000-72052800	Strong transcription	Fetal Intestine Large	intestine
40	chr16:72046000-72053400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:72046000-72060200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr16:72046000-72064000	Strong transcription	Primary T cells from cord blood	blood
43	chr16:72046200-72052800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr16:72046200-72052800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr16:72046200-72053400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr16:72046200-72053800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr16:72046400-72053800	Strong transcription	Brain Germinal Matrix	brain
48	chr16:72046400-72060200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr16:72046400-72062200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:72046600-72050600	Genic enhancers	Fetal Muscle Leg	muscle

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