Variant report

Variant	rs8044555
Chromosome Location	chr16:72152755-72152756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72151651..72153168-chr16:72156132..72159104,2	MCF-7	breast:
2	chr16:72144522..72146740-chr16:72151105..72152934,2	K562	blood:

Variant related genes	Relation type
ENSG00000118557	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10492813	0.95[JPT][hapmap]
rs10492814	0.89[JPT][hapmap]
rs1050361	0.95[JPT][hapmap]
rs1050362	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1050363	0.90[JPT][hapmap]
rs11075922	0.89[ASN][1000 genomes]
rs12325142	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12444701	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12445401	0.85[ASN][1000 genomes]
rs12445586	0.88[ASN][1000 genomes]
rs12448315	0.89[ASN][1000 genomes]
rs12708926	0.88[ASN][1000 genomes]
rs12708927	0.88[ASN][1000 genomes]
rs12708928	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12924413	0.95[JPT][hapmap]
rs12928732	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12933838	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13334151	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16973716	0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2000999	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2072141	0.95[JPT][hapmap]
rs2072142	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2074626	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2074627	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2240243	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2241411	0.81[JPT][hapmap]
rs2241412	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2287997	0.90[ASN][1000 genomes]
rs2303285	0.95[JPT][hapmap]
rs2550035	0.95[JPT][hapmap]
rs2550038	0.89[JPT][hapmap]
rs28432692	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854956	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3213422	0.93[YRI][hapmap]
rs34714490	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35460163	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35959677	0.90[EUR][1000 genomes]
rs3764311	0.95[JPT][hapmap]
rs3764312	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3764314	0.95[JPT][hapmap]
rs3812987	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3852781	0.95[JPT][hapmap]
rs3902135	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909543	0.81[ASN][1000 genomes]
rs4238964	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs4788597	0.93[YRI][hapmap]
rs56960650	0.84[ASN][1000 genomes]
rs57186116	0.83[ASN][1000 genomes]
rs6416742	0.91[ASN][1000 genomes]
rs6499559	0.90[ASN][1000 genomes]
rs6499560	0.90[ASN][1000 genomes]
rs6499561	0.83[ASN][1000 genomes]
rs6499562	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6680	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7184169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7186207	0.86[YRI][hapmap]
rs7188058	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190995	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7191127	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7192730	0.88[ASN][1000 genomes]
rs7198572	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7940	0.81[JPT][hapmap]
rs8044868	0.81[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs8045481	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8047377	0.91[ASN][1000 genomes]
rs8050238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8051882	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8052338	0.81[ASN][1000 genomes]
rs8052408	0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs8058609	0.85[ASN][1000 genomes]
rs8059378	0.88[ASN][1000 genomes]
rs8059437	0.81[JPT][hapmap]
rs8061282	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8061459	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062041	0.94[JPT][hapmap]
rs929866	0.86[YRI][hapmap]
rs9923344	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9925763	0.91[ASN][1000 genomes]
rs9926156	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9926927	0.95[JPT][hapmap]
rs9928157	0.81[JPT][hapmap]
rs9932951	0.81[JPT][hapmap]
rs9933009	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9941087	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.88[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8044555	HP	cis	parietal	SCAN
rs8044555	HP	cis	cerebellum	SCAN
rs8044555	FAM65A	cis	cerebellum	SCAN
rs8044555	DHODH	cis	cerebellum	SCAN
rs8044555	DHX38	cis	lymphoblastoid	seeQTL
rs8044555	HPR	cis	parietal	SCAN
rs8044555	NRN1L	cis	parietal	SCAN
rs8044555	DHX38	cis	Lymphoblastoid	GTEx
rs8044555	DHX38	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72142800-72158600	Weak transcription	Fetal Brain Male	brain
2	chr16:72145800-72156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:72145800-72160400	Weak transcription	HMEC	breast
4	chr16:72146400-72158600	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:72146400-72159000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:72146600-72152800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:72146600-72154600	Weak transcription	HUVEC	blood vessel
8	chr16:72146600-72155000	Weak transcription	Stomach Mucosa	stomach
9	chr16:72146600-72159000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr16:72146600-72159200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr16:72146600-72166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:72146800-72158400	Weak transcription	HepG2	liver
13	chr16:72146800-72158600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr16:72146800-72159000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr16:72146800-72159200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr16:72147000-72155600	Weak transcription	NHEK	skin
17	chr16:72147000-72158600	Weak transcription	Ovary	ovary
18	chr16:72147000-72158800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr16:72147000-72158800	Weak transcription	Brain Angular Gyrus	brain
20	chr16:72147000-72159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr16:72147000-72164800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr16:72147000-72172200	Weak transcription	Dnd41	blood
23	chr16:72147200-72158600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr16:72147200-72158600	Weak transcription	Brain Substantia Nigra	brain
25	chr16:72147200-72158600	Weak transcription	GM12878-XiMat	blood
26	chr16:72147200-72158800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:72147200-72159000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr16:72147200-72159000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:72147200-72159000	Weak transcription	Fetal Lung	lung
30	chr16:72147200-72159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr16:72147400-72158200	Weak transcription	Spleen	Spleen
32	chr16:72147400-72158600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:72147400-72158800	Weak transcription	Fetal Thymus	thymus
34	chr16:72147400-72159000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr16:72147400-72159000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:72147400-72159000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr16:72147400-72159000	Weak transcription	Fetal Brain Female	brain
38	chr16:72147400-72159000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr16:72147400-72159200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr16:72147400-72159200	Weak transcription	Pancreas	Pancrea
41	chr16:72147400-72162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:72147400-72164800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:72147600-72153000	Weak transcription	Gastric	stomach
44	chr16:72147600-72153400	Weak transcription	NHLF	lung
45	chr16:72147600-72158400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr16:72147600-72158400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr16:72147600-72158600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:72147600-72158800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr16:72147600-72159000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr16:72147600-72159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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