Variant report

Variant	rs72717854
Chromosome Location	chr1:171566113-171566114
allele	A/C
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10913119	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913149	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913157	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913285	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913292	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12564279	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12567152	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2038040	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038041	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038043	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294291	0.86[ASN][1000 genomes]
rs3204333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57562814	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60014783	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6669168	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6676140	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681173	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702038	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717832	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72717839	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72717840	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72717853	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517178	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521480	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7522026	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171524400-171566400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:171529600-171566200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171554400-171568400	Weak transcription	Psoas Muscle	Psoas
4	chr1:171556800-171567600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:171558800-171573200	Weak transcription	Small Intestine	intestine
6	chr1:171561200-171569800	Weak transcription	Pancreas	Pancrea
7	chr1:171561600-171570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:171561600-171572200	Weak transcription	Aorta	Aorta
9	chr1:171561800-171566200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:171561800-171567000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:171561800-171567600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:171561800-171568000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:171561800-171568000	Weak transcription	K562	blood
14	chr1:171561800-171570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:171561800-171570200	Weak transcription	Lung	lung
16	chr1:171561800-171570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:171561800-171572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:171561800-171576600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:171562000-171568000	Weak transcription	Thymus	Thymus
20	chr1:171562000-171568200	Weak transcription	NHDF-Ad	bronchial
21	chr1:171562000-171569000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:171562000-171572000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:171562200-171571800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:171562200-171575600	Weak transcription	HepG2	liver
25	chr1:171562600-171566200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:171562800-171572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:171562800-171572200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:171563200-171572000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:171563400-171566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:171563600-171566400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:171563600-171566600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:171563800-171566400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:171563800-171566600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:171563800-171566800	Enhancers	Liver	Liver
35	chr1:171563800-171567000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:171563800-171568400	Weak transcription	Fetal Brain Female	brain
37	chr1:171564000-171567000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:171564000-171567400	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:171564000-171568000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:171564000-171568000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:171564000-171572200	Weak transcription	Fetal Kidney	kidney
42	chr1:171564200-171567000	Weak transcription	Brain Germinal Matrix	brain
43	chr1:171564200-171567600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:171564400-171567200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:171564400-171567600	Weak transcription	Fetal Thymus	thymus
46	chr1:171564400-171568600	Weak transcription	NH-A	brain
47	chr1:171564400-171569400	Weak transcription	Brain Anterior Caudate	brain
48	chr1:171564400-171570600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:171564400-171572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:171564400-171573000	Weak transcription	Adipose Nuclei	Adipose

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