Variant report

Variant	rs203461
Chromosome Location	chr17:19813468-19813469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11204419	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204420	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204421	0.82[ASN][1000 genomes]
rs119672	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479129	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166840	0.85[EUR][1000 genomes]
rs169412	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175921	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191865	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203450	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203451	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203452	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203455	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs203456	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203457	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203458	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203459	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203460	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203462	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203465	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203466	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203469	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203470	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203479	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203481	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203482	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2108978	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs397969	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427798	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925060	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56153261	0.86[ASN][1000 genomes]
rs6587206	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7222403	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066150	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs850623	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860335	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907752	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9914273	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9914304	0.90[EUR][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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs203461	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19801400-19814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:19801600-19814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:19802200-19814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
6	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:19803000-19822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr17:19803000-19824400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
12	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:19803600-19814000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:19803600-19826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:19803800-19818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:19803800-19822400	Strong transcription	Primary T cells from cord blood	blood
20	chr17:19803800-19823400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr17:19803800-19824000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:19804000-19823600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:19804000-19853000	Strong transcription	Dnd41	blood
26	chr17:19805400-19814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:19805600-19823800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:19805800-19824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr17:19806800-19813600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:19806800-19813800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:19806800-19814000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:19806800-19814000	Strong transcription	Brain Substantia Nigra	brain
37	chr17:19806800-19814200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:19807000-19825800	Strong transcription	Placenta	Placenta
39	chr17:19807200-19823400	Strong transcription	Thymus	Thymus
40	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:19808000-19823600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:19808200-19815000	Strong transcription	Left Ventricle	heart
43	chr17:19808200-19828400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:19808400-19813800	Strong transcription	NHEK	skin
45	chr17:19808400-19823000	Strong transcription	Brain Hippocampus Middle	brain
46	chr17:19808400-19823000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr17:19808400-19823800	Strong transcription	Fetal Lung	lung
48	chr17:19808600-19814800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr17:19808600-19815200	Strong transcription	Ovary	ovary
50	chr17:19808600-19818600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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