Variant report

Variant	rs171376
Chromosome Location	chr19:38266993-38266994
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	chr19:38265404..38267660-chr19:38268502..38271675,3	K562	blood:
2	chr19:38266556..38268696-chr19:44667291..44670054,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267422	Chromatin interaction
ENSG00000167380	Chromatin interaction
ENSG00000189144	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10048511	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10401968	0.84[EUR][1000 genomes]
rs10402530	0.83[EUR][1000 genomes]
rs10409402	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10409487	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420746	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420891	0.83[EUR][1000 genomes]
rs11673023	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11878269	0.84[EUR][1000 genomes]
rs11879180	0.83[EUR][1000 genomes]
rs1291	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12974225	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12975057	0.83[EUR][1000 genomes]
rs1974714	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075281	0.84[EUR][1000 genomes]
rs2075284	0.80[ASN][1000 genomes]
rs2287229	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs241932	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs241933	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs241950	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909093	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2909098	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2909100	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972434	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972437	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972438	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972439	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972445	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3095724	0.81[ASN][1000 genomes]
rs3095726	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112434	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3848626	0.83[EUR][1000 genomes]
rs4802135	0.81[EUR][1000 genomes]
rs4803509	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803524	0.83[EUR][1000 genomes]
rs6508742	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257125	0.84[EUR][1000 genomes]
rs8101752	0.83[EUR][1000 genomes]
rs8101858	0.80[EUR][1000 genomes]
rs8102579	0.83[EUR][1000 genomes]
rs8103633	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104076	0.84[EUR][1000 genomes]
rs8112706	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8182498	0.83[EUR][1000 genomes]
rs856300	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs856304	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304569	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958305	0.81[EUR][1000 genomes]
rs968073	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs171376	WDR87	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
2	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
3	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
4	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
5	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
7	chr19:38248800-38269400	Weak transcription	NH-A	brain
8	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
9	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:38251800-38269400	Weak transcription	Gastric	stomach
11	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
12	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:38252600-38269000	Weak transcription	NHEK	skin
14	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
15	chr19:38254800-38269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:38256800-38269400	Weak transcription	NHLF	lung
17	chr19:38258400-38267600	Weak transcription	K562	blood
18	chr19:38258800-38269200	Weak transcription	HSMMtube	muscle
19	chr19:38259200-38269200	Weak transcription	Brain Angular Gyrus	brain
20	chr19:38259200-38269200	Weak transcription	Fetal Kidney	kidney
21	chr19:38259200-38269200	Weak transcription	HSMM	muscle
22	chr19:38259200-38269400	Weak transcription	Psoas Muscle	Psoas
23	chr19:38259400-38269200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:38260200-38269000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:38260200-38269200	Weak transcription	Fetal Thymus	thymus
26	chr19:38260800-38269000	Weak transcription	Thymus	Thymus
27	chr19:38260800-38269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:38260800-38269200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:38260800-38269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:38260800-38269400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:38261000-38269000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:38261000-38269200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:38261000-38269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:38261000-38269200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr19:38261000-38269200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:38261200-38269000	Weak transcription	Pancreas	Pancrea
37	chr19:38261200-38269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:38261200-38269200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:38261200-38269200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:38261200-38269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38261200-38269200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:38261200-38269200	Weak transcription	HepG2	liver
43	chr19:38261200-38269200	Weak transcription	Osteobl	bone
44	chr19:38261200-38269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:38261200-38269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:38261200-38269400	Weak transcription	Esophagus	oesophagus
47	chr19:38261200-38269400	Weak transcription	Fetal Muscle Leg	muscle
48	chr19:38261200-38269400	Weak transcription	Placenta	Placenta
49	chr19:38261200-38269400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:38261400-38268800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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