Variant report

Variant	rs2144545
Chromosome Location	chr20:1415177-1415178
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
2	chr20:1406951..1409518-chr20:1413752..1415775,2	K562	blood:
3	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
4	chr20:1409886..1412172-chr20:1413671..1415589,2	K562	blood:
5	chr20:1405728..1407229-chr20:1414214..1416774,2	MCF-7	breast:
6	chr20:1414416..1417829-chr20:1445784..1450800,6	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1028508	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11087052	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs11699735	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1884388	0.84[ASN][1000 genomes]
rs1884389	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884391	0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2144542	0.80[ASN][1000 genomes]
rs2144543	0.80[ASN][1000 genomes]
rs2144544	0.96[ASN][1000 genomes]
rs2144546	0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2317513	0.92[ASN][1000 genomes]
rs2317651	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2317652	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088080	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3171292	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3210915	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs36018423	0.80[ASN][1000 genomes]
rs3795135	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3829698	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4352285	0.83[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4546067	0.83[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4813133	0.84[JPT][hapmap]
rs4814237	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4814240	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4814244	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs5019244	0.80[ASN][1000 genomes]
rs6033710	0.89[JPT][hapmap]
rs6033715	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6033726	0.80[ASN][1000 genomes]
rs6033728	0.80[ASN][1000 genomes]
rs6033729	0.80[ASN][1000 genomes]
rs6033732	0.80[ASN][1000 genomes]
rs6033744	0.80[ASN][1000 genomes]
rs6033807	0.92[ASW][hapmap];0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042117	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042118	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042131	0.80[ASN][1000 genomes]
rs6042160	0.80[ASN][1000 genomes]
rs6042170	0.80[ASN][1000 genomes]
rs6042172	0.80[ASN][1000 genomes]
rs6042175	0.80[ASN][1000 genomes]
rs6042207	0.80[ASN][1000 genomes]
rs6042208	0.80[ASN][1000 genomes]
rs6042238	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042244	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6042268	0.96[ASN][1000 genomes]
rs6042270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042283	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042292	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042354	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6074631	0.84[ASN][1000 genomes]
rs6079133	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079138	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079139	0.95[ASN][1000 genomes]
rs6105102	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6105110	0.84[JPT][hapmap]
rs6105165	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109893	0.80[ASN][1000 genomes]
rs6109894	0.80[ASN][1000 genomes]
rs6109912	0.80[ASN][1000 genomes]
rs6131506	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131519	0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6134916	0.80[ASN][1000 genomes]
rs6891	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs750424	0.80[ASN][1000 genomes]
rs8124053	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs910619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910620	0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs932524	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9575	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2144545	NSFL1C	cis	Frontal Cortex	GTEx
rs2144545	NSFL1C	cis	cerebellum	SCAN
rs2144545	NSFL1C	cis	Temporal Cortex	GTEx
rs2144545	NSFL1C	cis	lymphoblastoid	seeQTL
rs2144545	TGM3	cis	cerebellum	SCAN
rs2144545	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs2144545	NSFL1C	cis	Brain Pons	GTEx
rs2144545	DEFB125	cis	cerebellum	SCAN
rs2144545	NSFL1C	cis	multi-tissue	Pritchard
rs2144545	NSFL1C	cis	Cerebellum	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
2	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
3	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
7	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
8	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
9	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
17	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
18	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
19	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:1411000-1415200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:1411000-1415200	Weak transcription	NHEK	skin
22	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
23	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
24	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:1411400-1415200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:1411400-1415200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
30	chr20:1412000-1415200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:1412400-1419000	Weak transcription	Brain Hippocampus Middle	brain
32	chr20:1412800-1415400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr20:1412800-1420200	Weak transcription	Ovary	ovary
34	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
35	chr20:1413400-1415200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr20:1413600-1415200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr20:1413800-1419200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr20:1413800-1420400	Weak transcription	Gastric	stomach
39	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
40	chr20:1414200-1415400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
41	chr20:1414200-1415600	Strong transcription	A549	lung
42	chr20:1414200-1416000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr20:1414400-1415200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:1414400-1415200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr20:1414400-1416000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr20:1414400-1416200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr20:1414400-1416800	Enhancers	Primary hematopoietic stem cells	blood
48	chr20:1414400-1416800	Enhancers	Dnd41	blood
49	chr20:1414600-1415200	Enhancers	Primary B cells from cord blood	blood
50	chr20:1414600-1415200	ZNF genes & repeats	Fetal Muscle Leg	muscle

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