Variant report

Variant	rs6953
Chromosome Location	chr3:191116133-191116134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191109601..191112408-chr3:191114470..191116944,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PYDC2-5	chr3:191113180-191116458	NONHSAT093967

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10937477	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs13061649	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1347400	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1465737	0.86[EUR][1000 genomes]
rs1473866	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs150506	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159488	0.87[ASN][1000 genomes]
rs159489	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656143	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1662184	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs167148	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176820	0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176821	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176822	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs184140	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186063	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs186064	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186065	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188385	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs192671	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs211043	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2572064	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293797	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs293798	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs293800	0.91[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293802	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293804	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293805	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293806	0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293807	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293808	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293809	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293810	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293811	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293812	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293813	0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293814	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293815	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs293837	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293839	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293840	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293841	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293844	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293846	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293851	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297396	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs364519	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs366626	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs367747	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368665	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369174	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373035	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381090	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383075	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383529	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs386241	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs389765	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs390744	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392311	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs399575	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs401465	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs403078	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs407226	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs415149	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs420266	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs426466	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429374	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs429521	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs432085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434556	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436393	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs436428	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs437244	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438589	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs441509	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs445914	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs447931	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs448133	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs448643	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs449398	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4677630	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4677734	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4677735	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491252	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs513632	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs520494	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs520600	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs523270	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs525774	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526785	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529523	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566548	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568702	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs578401	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6779820	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs697905	0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709142	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847278	0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6953	CCDC50	cis	Artery Tibial	GTEx
rs6953	CCDC50	cis	Artery Aorta	GTEx
rs6953	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:191079600-191121200	Weak transcription	Gastric	stomach
3	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
4	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
7	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
9	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
12	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
13	chr3:191100200-191119600	Weak transcription	K562	blood
14	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
15	chr3:191100400-191117400	Weak transcription	Lung	lung
16	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
17	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
18	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
19	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:191101200-191117000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
23	chr3:191104800-191116600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:191106800-191117200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:191107400-191117200	Weak transcription	HepG2	liver
26	chr3:191108000-191117400	Weak transcription	NHEK	skin
27	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
29	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
30	chr3:191109200-191117600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:191109600-191116400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:191110600-191117600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:191110600-191117600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:191111000-191117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:191111200-191118000	Weak transcription	Fetal Lung	lung
39	chr3:191111400-191117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:191111400-191117800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:191111400-191117800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:191112000-191116600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:191112000-191118000	Strong transcription	Adipose Nuclei	Adipose
44	chr3:191112200-191116600	Strong transcription	Liver	Liver
45	chr3:191112200-191118400	Strong transcription	NH-A	brain
46	chr3:191112400-191117200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:191112600-191116600	Strong transcription	Osteobl	bone
48	chr3:191113200-191118200	Weak transcription	Hela-S3	cervix
49	chr3:191113600-191118200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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