Variant report

Variant	rs188385
Chromosome Location	chr3:191117285-191117286
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10937477	0.85[ASN][1000 genomes]
rs1347400	0.87[ASN][1000 genomes]
rs1473866	0.85[ASN][1000 genomes]
rs150506	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159488	0.83[ASN][1000 genomes]
rs159489	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs186066	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs188384	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs293797	0.87[ASN][1000 genomes]
rs293798	0.85[ASN][1000 genomes]
rs293800	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs293802	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293804	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs293805	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293806	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs293808	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293815	0.87[ASN][1000 genomes]
rs293844	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293846	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs293851	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs297396	0.87[ASN][1000 genomes]
rs366626	0.89[ASN][1000 genomes]
rs367747	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs368665	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs369174	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs373035	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs381090	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383075	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390744	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401465	0.87[ASN][1000 genomes]
rs426466	0.96[ASN][1000 genomes]
rs432085	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434556	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437244	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs448133	0.87[ASN][1000 genomes]
rs4677630	0.87[ASN][1000 genomes]
rs4677734	0.83[ASN][1000 genomes]
rs4677735	0.85[ASN][1000 genomes]
rs523270	0.87[ASN][1000 genomes]
rs525774	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs526785	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs529523	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs566548	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779820	0.83[ASN][1000 genomes]
rs6953	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs697905	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709142	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847278	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs188385	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
11	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
12	chr3:191100200-191119600	Weak transcription	K562	blood
13	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
14	chr3:191100400-191117400	Weak transcription	Lung	lung
15	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
16	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
17	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
18	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
21	chr3:191108000-191117400	Weak transcription	NHEK	skin
22	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
24	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
25	chr3:191109200-191117600	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:191110600-191117600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:191110600-191117600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:191111000-191117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:191111200-191118000	Weak transcription	Fetal Lung	lung
33	chr3:191111400-191117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:191111400-191117800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:191111400-191117800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:191112000-191118000	Strong transcription	Adipose Nuclei	Adipose
37	chr3:191112200-191118400	Strong transcription	NH-A	brain
38	chr3:191113200-191118200	Weak transcription	Hela-S3	cervix
39	chr3:191113600-191118200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:191114200-191117400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:191114200-191118000	Weak transcription	NHDF-Ad	bronchial
43	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
44	chr3:191114200-191119400	Weak transcription	NHLF	lung
45	chr3:191114400-191117600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:191114400-191117600	Weak transcription	GM12878-XiMat	blood
47	chr3:191114400-191119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:191114400-191119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:191114400-191120400	Weak transcription	HSMM	muscle
50	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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