Variant report

Variant	rs9304572
Chromosome Location	chr19:38420606-38420607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38415914..38418453-chr19:38418940..38421267,2	MCF-7	breast:
2	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
3	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
4	chr19:38403265..38407111-chr19:38419790..38421668,3	MCF-7	breast:
5	chr19:38396701..38399337-chr19:38419695..38422490,2	K562	blood:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10401637	0.84[EUR][1000 genomes]
rs10402530	0.81[EUR][1000 genomes]
rs10404567	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420891	0.81[EUR][1000 genomes]
rs10427125	0.81[EUR][1000 genomes]
rs11879180	0.81[EUR][1000 genomes]
rs12975057	0.81[EUR][1000 genomes]
rs1643462	0.86[EUR][1000 genomes]
rs1643463	0.86[EUR][1000 genomes]
rs1643466	0.86[EUR][1000 genomes]
rs1643467	0.86[EUR][1000 genomes]
rs1643468	0.86[EUR][1000 genomes]
rs1643469	0.89[EUR][1000 genomes]
rs1725477	0.86[EUR][1000 genomes]
rs1725478	0.86[EUR][1000 genomes]
rs1725480	0.86[EUR][1000 genomes]
rs1725481	0.86[EUR][1000 genomes]
rs1725482	0.86[EUR][1000 genomes]
rs1725483	0.86[EUR][1000 genomes]
rs1725485	0.86[EUR][1000 genomes]
rs1725487	0.86[EUR][1000 genomes]
rs1725488	0.85[EUR][1000 genomes]
rs1725494	0.88[EUR][1000 genomes]
rs2544718	0.88[EUR][1000 genomes]
rs35209753	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353398	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353399	0.91[EUR][1000 genomes]
rs353400	0.91[EUR][1000 genomes]
rs353402	0.91[EUR][1000 genomes]
rs353403	0.89[EUR][1000 genomes]
rs353404	0.91[EUR][1000 genomes]
rs353407	0.91[EUR][1000 genomes]
rs353414	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353415	0.87[EUR][1000 genomes]
rs353416	0.91[EUR][1000 genomes]
rs353417	0.91[EUR][1000 genomes]
rs353419	0.91[EUR][1000 genomes]
rs353420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353421	0.91[EUR][1000 genomes]
rs353423	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353424	0.91[EUR][1000 genomes]
rs353425	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353426	0.89[EUR][1000 genomes]
rs353427	0.91[EUR][1000 genomes]
rs353428	0.86[EUR][1000 genomes]
rs353429	0.84[EUR][1000 genomes]
rs353430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802135	0.82[EUR][1000 genomes]
rs4803524	0.81[EUR][1000 genomes]
rs705492	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs705494	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705500	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7250409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250571	0.84[EUR][1000 genomes]
rs7250868	0.84[EUR][1000 genomes]
rs7252010	0.83[EUR][1000 genomes]
rs7258597	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752878	0.86[EUR][1000 genomes]
rs8101858	0.81[EUR][1000 genomes]
rs8102579	0.81[EUR][1000 genomes]
rs8107341	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8110284	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8182498	0.81[EUR][1000 genomes]
rs833895	0.84[EUR][1000 genomes]
rs833896	0.85[EUR][1000 genomes]
rs833897	0.86[EUR][1000 genomes]
rs833898	0.86[EUR][1000 genomes]
rs833926	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription 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 lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv960761	chr19:38419928-38422738	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9304572	WDR87	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
6	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
10	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:38399800-38421200	Weak transcription	Gastric	stomach
12	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
13	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
14	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:38400000-38422000	Weak transcription	HSMM	muscle
16	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
18	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
19	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:38401000-38421600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:38401200-38421200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
23	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
24	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:38410200-38422200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:38410200-38422400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:38410400-38422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:38411600-38422600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:38411800-38421200	Weak transcription	NHEK	skin
31	chr19:38411800-38422200	Weak transcription	Brain Angular Gyrus	brain
32	chr19:38411800-38422200	Weak transcription	NH-A	brain
33	chr19:38411800-38422600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:38412000-38422000	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:38412000-38422600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:38412000-38423800	Weak transcription	Lung	lung
38	chr19:38412200-38421000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:38412200-38422600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38412200-38422800	Weak transcription	Adipose Nuclei	Adipose
41	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
42	chr19:38412400-38421200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:38412800-38422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:38413400-38421800	Weak transcription	Fetal Muscle Leg	muscle
45	chr19:38413400-38422000	Weak transcription	Fetal Stomach	stomach
46	chr19:38417000-38421000	Weak transcription	Osteobl	bone
47	chr19:38417200-38421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:38417600-38422600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:38417600-38422600	Weak transcription	Ovary	ovary
50	chr19:38418200-38422400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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