Variant report

Variant	rs6131506
Chromosome Location	chr20:1420757-1420758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
2	chr20:1418150..1421031-chr20:1445969..1448576,3	MCF-7	breast:
3	chr20:1315182..1316093-chr20:1420377..1420934,2	MCF-7	breast:
4	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
5	chr20:1419982..1421924-chr20:1432480..1435232,2	K562	blood:
6	chr20:1420460..1421270-chr20:1450721..1451369,3	MCF-7	breast:
7	chr20:1293582..1294335-chr20:1420417..1420965,2	MCF-7	breast:
8	chr20:1420415..1421693-chr20:1484065..1484901,6	MCF-7	breast:
9	chr20:1418037..1419774-chr20:1420141..1424100,3	MCF-7	breast:
10	chr20:1418229..1420990-chr20:1423275..1425647,2	MCF-7	breast:
11	chr20:1419111..1421909-chr20:1426787..1429297,2	MCF-7	breast:
12	chr20:1370272..1370827-chr20:1420141..1420942,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1028508	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11699735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063	0.96[ASN][1000 genomes]
rs1884388	0.83[ASN][1000 genomes]
rs1884389	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884391	0.95[ASN][1000 genomes]
rs2144544	0.95[ASN][1000 genomes]
rs2144545	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144546	0.93[ASN][1000 genomes]
rs2317513	0.93[ASN][1000 genomes]
rs2317651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2317652	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3088080	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3171292	0.96[ASN][1000 genomes]
rs3210915	0.96[ASN][1000 genomes]
rs3795135	0.84[ASN][1000 genomes]
rs3829698	0.93[ASN][1000 genomes]
rs4352285	0.96[ASN][1000 genomes]
rs4546067	0.96[ASN][1000 genomes]
rs6033807	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042238	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042244	0.95[ASN][1000 genomes]
rs6042268	0.95[ASN][1000 genomes]
rs6042270	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042292	0.96[ASN][1000 genomes]
rs6042354	0.95[ASN][1000 genomes]
rs6074631	0.83[ASN][1000 genomes]
rs6079133	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079138	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079139	0.96[ASN][1000 genomes]
rs6105165	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131519	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6891	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910619	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910620	0.96[ASN][1000 genomes]
rs932524	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9575	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6131506	NSFL1C	cis	Brain Pons	GTEx
rs6131506	NSFL1C	cis	Frontal Cortex	GTEx
rs6131506	NSFL1C	cis	Cerebellum	GTEx
rs6131506	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs6131506	NSFL1C	cis	multi-tissue	Pritchard
rs6131506	NSFL1C	cis	Temporal Cortex	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
3	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
4	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
8	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
9	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
10	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
12	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:1415200-1422800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr20:1415400-1421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr20:1415400-1422400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:1415400-1422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr20:1415600-1422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:1415600-1423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:1415800-1422000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:1416000-1421000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:1416000-1421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:1416000-1421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:1416000-1422000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:1416000-1422000	Weak transcription	HSMM	muscle
25	chr20:1416000-1422000	Weak transcription	NH-A	brain
26	chr20:1416000-1422200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:1416000-1422400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr20:1416000-1422400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr20:1416000-1422400	Weak transcription	Small Intestine	intestine
30	chr20:1416200-1420800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr20:1416200-1421600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr20:1416200-1421800	Weak transcription	HMEC	breast
33	chr20:1416200-1422200	Weak transcription	HSMMtube	muscle
34	chr20:1416200-1422600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:1416200-1422600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:1416200-1422600	Weak transcription	NHEK	skin
37	chr20:1416200-1423200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:1416400-1421200	Weak transcription	Thymus	Thymus
39	chr20:1416400-1421400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr20:1416400-1421600	Weak transcription	Fetal Thymus	thymus
41	chr20:1416400-1422000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr20:1416400-1422400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr20:1416400-1422400	Weak transcription	GM12878-XiMat	blood
44	chr20:1416600-1422400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr20:1416800-1421600	Weak transcription	Dnd41	blood
46	chr20:1416800-1422200	Weak transcription	Osteobl	bone
47	chr20:1416800-1422600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr20:1416800-1422600	Weak transcription	NHDF-Ad	bronchial
49	chr20:1416800-1424200	Weak transcription	K562	blood
50	chr20:1417000-1422400	Weak transcription	Muscle Satellite Cultured Cells	--

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