Variant report

Variant	rs235884
Chromosome Location	chr1:171567339-171567340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRRC2C-2	chr1:171564842-171568051	NONHSAT007539

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10753119	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753120	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753121	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753126	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913176	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913198	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs116358	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13722	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626990	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1687057	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1687060	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1687061	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1687064	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs170969	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs170970	0.81[AMR][1000 genomes]
rs182897	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015996	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2038042	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179141	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207193	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2223898	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272809	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294289	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235465	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs235466	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs235467	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235468	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235469	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235470	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235473	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235474	0.81[EUR][1000 genomes]
rs235476	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235480	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235481	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235482	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235484	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235485	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs235487	1.00[ASN][1000 genomes]
rs235489	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235491	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235492	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235493	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235494	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235497	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235499	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs235500	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235501	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235503	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235504	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235505	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235506	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235508	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235509	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235510	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235883	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235885	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235887	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235905	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235906	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235907	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235908	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421841	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4276951	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4384265	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916230	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916231	0.96[ASN][1000 genomes]
rs4916232	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4916389	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4916391	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916392	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916393	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916394	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61814663	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61814673	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697306	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702990	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514441	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7523355	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535195	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536075	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7538827	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7548158	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760643	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs760644	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954035	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235884	DNM3OS	cis	Artery Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171554400-171568400	Weak transcription	Psoas Muscle	Psoas
2	chr1:171556800-171567600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:171558800-171573200	Weak transcription	Small Intestine	intestine
4	chr1:171561200-171569800	Weak transcription	Pancreas	Pancrea
5	chr1:171561600-171570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:171561600-171572200	Weak transcription	Aorta	Aorta
7	chr1:171561800-171567600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:171561800-171568000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:171561800-171568000	Weak transcription	K562	blood
10	chr1:171561800-171570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:171561800-171570200	Weak transcription	Lung	lung
12	chr1:171561800-171570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:171561800-171572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:171561800-171576600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:171562000-171568000	Weak transcription	Thymus	Thymus
16	chr1:171562000-171568200	Weak transcription	NHDF-Ad	bronchial
17	chr1:171562000-171569000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:171562000-171572000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:171562200-171571800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:171562200-171575600	Weak transcription	HepG2	liver
21	chr1:171562800-171572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:171562800-171572200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:171563200-171572000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:171563800-171568400	Weak transcription	Fetal Brain Female	brain
25	chr1:171564000-171567400	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:171564000-171568000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:171564000-171568000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:171564000-171572200	Weak transcription	Fetal Kidney	kidney
29	chr1:171564200-171567600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr1:171564400-171567600	Weak transcription	Fetal Thymus	thymus
31	chr1:171564400-171568600	Weak transcription	NH-A	brain
32	chr1:171564400-171569400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:171564400-171570600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:171564400-171572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:171564400-171573000	Weak transcription	Adipose Nuclei	Adipose
36	chr1:171564600-171567400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:171564600-171568200	Weak transcription	Osteobl	bone
38	chr1:171564600-171568400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:171564800-171569400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:171564800-171570200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:171565000-171569000	Weak transcription	Primary T cells from cord blood	blood
42	chr1:171565600-171567400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:171566200-171572000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:171566400-171568600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:171566800-171568800	Weak transcription	GM12878-XiMat	blood
46	chr1:171566800-171569400	Weak transcription	Liver	Liver
47	chr1:171567000-171567800	Weak transcription	HSMM	muscle
48	chr1:171567000-171569000	Weak transcription	Primary B cells from cord blood	blood

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