Variant report

Variant	rs6079139
Chromosome Location	chr20:1422265-1422266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
2	chr20:1422067..1424676-chr20:1434569..1437810,4	K562	blood:
3	chr20:1418037..1419774-chr20:1420141..1424100,3	MCF-7	breast:
4	chr20:1422183..1425116-chr20:1445369..1447221,2	K562	blood:
5	chr20:1422067..1424676-chr20:1434569..1437810,3	K562	blood:
6	chr20:1421730..1423877-chr20:1425978..1428571,2	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1028508	0.95[ASN][1000 genomes]
rs11699578	1.00[JPT][hapmap]
rs11699735	0.96[ASN][1000 genomes]
rs13063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884388	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884389	0.83[ASN][1000 genomes]
rs1884391	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144544	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144545	0.95[ASN][1000 genomes]
rs2144546	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317513	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317651	0.80[ASN][1000 genomes]
rs2317652	0.95[ASN][1000 genomes]
rs3088080	0.96[ASN][1000 genomes]
rs3171292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210915	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795135	0.81[ASN][1000 genomes]
rs3829698	0.89[ASN][1000 genomes]
rs4352285	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546067	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033807	0.96[ASN][1000 genomes]
rs6042238	0.95[ASN][1000 genomes]
rs6042244	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042268	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042270	0.95[ASN][1000 genomes]
rs6042283	0.95[ASN][1000 genomes]
rs6042292	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042354	0.99[ASN][1000 genomes]
rs6074631	0.80[ASN][1000 genomes]
rs6079133	0.96[ASN][1000 genomes]
rs6079138	0.96[ASN][1000 genomes]
rs6105165	0.95[ASN][1000 genomes]
rs6131506	0.96[ASN][1000 genomes]
rs6891	0.96[ASN][1000 genomes]
rs910619	0.95[ASN][1000 genomes]
rs910620	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932524	0.96[ASN][1000 genomes]
rs9575	0.95[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	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	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6079139	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs6079139	NSFL1C	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
2	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
3	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
7	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
8	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
9	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
10	chr20:1415200-1422800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr20:1415400-1422400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:1415400-1422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr20:1415600-1422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:1415600-1423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr20:1416000-1422400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr20:1416000-1422400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr20:1416000-1422400	Weak transcription	Small Intestine	intestine
18	chr20:1416200-1422600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:1416200-1422600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:1416200-1422600	Weak transcription	NHEK	skin
21	chr20:1416200-1423200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:1416400-1422400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr20:1416400-1422400	Weak transcription	GM12878-XiMat	blood
24	chr20:1416600-1422400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr20:1416800-1422600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:1416800-1422600	Weak transcription	NHDF-Ad	bronchial
27	chr20:1416800-1424200	Weak transcription	K562	blood
28	chr20:1417000-1422400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr20:1417000-1424600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr20:1417800-1422800	Weak transcription	HUVEC	blood vessel
31	chr20:1418400-1422600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr20:1418400-1422800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr20:1418600-1425000	Weak transcription	Fetal Heart	heart
34	chr20:1419000-1430600	Strong transcription	Fetal Stomach	stomach
35	chr20:1419000-1431400	Strong transcription	Brain Germinal Matrix	brain
36	chr20:1419000-1431800	Strong transcription	Brain Hippocampus Middle	brain
37	chr20:1419200-1430200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr20:1419200-1431800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr20:1419200-1443400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr20:1419600-1428800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr20:1419600-1429200	Strong transcription	Fetal Muscle Leg	muscle
42	chr20:1419600-1431000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr20:1419600-1432000	Strong transcription	Fetal Intestine Large	intestine
44	chr20:1419600-1442000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr20:1419800-1430000	Strong transcription	Brain Anterior Caudate	brain
46	chr20:1419800-1443600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr20:1420000-1431400	Strong transcription	Fetal Brain Female	brain
48	chr20:1420000-1431600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr20:1420000-1431600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr20:1420000-1431800	Strong transcription	Brain Inferior Temporal Lobe	brain

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