Variant report

Variant	rs1050363
Chromosome Location	chr16:72135014-72135015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:72134986-72135365	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72133291..72136236-chr16:72141533..72144792,4	K562	blood:
2	chr16:72134347..72135953-chr16:72140666..72142742,2	MCF-7	breast:

Variant related genes	Relation type
DHX38	TF binding region
ENSG00000140829	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10492813	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10492814	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1050361	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1050362	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs10852511	0.90[JPT][hapmap]
rs11075924	0.81[ASW][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs11862813	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12325142	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs12449073	0.81[YRI][hapmap]
rs12708925	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12708928	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs12924413	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12928732	0.85[JPT][hapmap]
rs12932845	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12935266	0.80[CEU][hapmap]
rs13334151	0.85[JPT][hapmap]
rs1465457	0.93[YRI][hapmap]
rs16973716	0.85[JPT][hapmap]
rs2000999	0.84[JPT][hapmap]
rs2070937	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2070939	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs2072141	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2072142	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs2074626	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs2074627	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs217181	1.00[YRI][hapmap]
rs2240243	0.82[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs2241411	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241412	0.88[ASW][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs2269918	0.96[ASN][1000 genomes]
rs2288000	0.87[CHB][hapmap]
rs2288002	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2303285	0.87[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2550035	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2550038	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs2550868	0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2854956	0.90[JPT][hapmap]
rs3764311	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3764312	0.85[JPT][hapmap]
rs3764314	0.81[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3812984	0.80[JPT][hapmap]
rs3812986	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3812987	0.90[JPT][hapmap]
rs3844425	0.87[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs3852781	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3852782	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3852784	0.81[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs3902135	0.85[JPT][hapmap]
rs3909541	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs4788461	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4788609	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs4788610	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6499562	0.85[JPT][hapmap]
rs6680	0.87[ASW][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs7184169	0.90[JPT][hapmap]
rs7188058	0.85[JPT][hapmap]
rs7190995	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs7191127	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs7194397	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7194668	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7198572	0.85[JPT][hapmap]
rs7201643	0.87[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7203426	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7203821	0.83[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7940	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8043606	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs8044555	0.90[JPT][hapmap]
rs8044868	0.85[JPT][hapmap]
rs8047377	0.81[ASN][1000 genomes]
rs8050238	0.90[JPT][hapmap]
rs8051882	0.88[ASW][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs8052408	0.85[JPT][hapmap]
rs8059437	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8060770	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8062041	0.83[JPT][hapmap]
rs8062895	0.93[YRI][hapmap]
rs9924964	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9925763	0.81[ASN][1000 genomes]
rs9926156	0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9926927	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9927526	0.86[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap]
rs9928157	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9930890	0.86[ASN][1000 genomes]
rs9932062	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9932951	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs9941087	0.90[JPT][hapmap]
rs9941346	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]

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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1050363	HPR	cis	parietal	SCAN
rs1050363	DHODH	cis	cerebellum	SCAN
rs1050363	DHX38	cis	lymphoblastoid	seeQTL
rs1050363	HP	cis	parietal	SCAN
rs1050363	OR4D11	trans	cerebellum	SCAN
rs1050363	HPR	cis	cerebellum	SCAN
rs1050363	NRN1L	cis	parietal	SCAN
rs1050363	FAM65A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72128800-72136000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:72129400-72138800	Weak transcription	Right Atrium	heart
3	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
4	chr16:72129600-72135600	Strong transcription	Primary B cells from cord blood	blood
5	chr16:72129800-72135400	Weak transcription	Fetal Heart	heart
6	chr16:72129800-72145600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:72129800-72146000	Strong transcription	HSMMtube	muscle
8	chr16:72129800-72146600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr16:72129800-72147000	Strong transcription	Ovary	ovary
10	chr16:72129800-72147200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:72130000-72135600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr16:72130000-72137000	Strong transcription	NHDF-Ad	bronchial
17	chr16:72130000-72139000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
18	chr16:72130000-72140600	Strong transcription	Fetal Kidney	kidney
19	chr16:72130000-72140600	Strong transcription	K562	blood
20	chr16:72130000-72144800	Strong transcription	Fetal Intestine Large	intestine
21	chr16:72130000-72144800	Strong transcription	Fetal Intestine Small	intestine
22	chr16:72130000-72145600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr16:72130000-72146400	Strong transcription	Colon Smooth Muscle	Colon
24	chr16:72130000-72146600	Strong transcription	HUVEC	blood vessel
25	chr16:72130000-72146800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr16:72130000-72146800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr16:72130000-72147000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr16:72130000-72147000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:72130000-72147000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr16:72130000-72147000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:72130000-72147000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:72130000-72147000	Strong transcription	Esophagus	oesophagus
33	chr16:72130000-72147000	Strong transcription	NHEK	skin
34	chr16:72130000-72147200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr16:72130000-72147200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr16:72130000-72147200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:72130000-72147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:72130000-72147200	Strong transcription	Aorta	Aorta
39	chr16:72130000-72147200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr16:72130000-72147200	Strong transcription	Brain Substantia Nigra	brain
41	chr16:72130000-72147200	Strong transcription	Fetal Lung	lung
42	chr16:72130000-72147200	Strong transcription	Left Ventricle	heart
43	chr16:72130000-72147400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr16:72130000-72147400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr16:72130000-72147400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:72130000-72147400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr16:72130000-72147400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr16:72130000-72147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr16:72130000-72147400	Strong transcription	Adipose Nuclei	Adipose
50	chr16:72130000-72147400	Strong transcription	Duodenum Mucosa	Duodenum

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