Variant report

Variant	rs6042207
Chromosome Location	chr20:1406136-1406137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1403838..1406635-chr20:1407133..1408659,2	K562	blood:
2	chr20:1405279..1407726-chr20:1449432..1451429,2	K562	blood:
3	chr20:1405728..1407229-chr20:1414214..1416774,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1028508	0.80[ASN][1000 genomes]
rs11087052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884388	0.86[ASN][1000 genomes]
rs1884389	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1998007	0.85[ASN][1000 genomes]
rs2144542	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144543	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144545	0.80[CEU][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2207829	0.85[ASN][1000 genomes]
rs2207830	0.97[ASN][1000 genomes]
rs2317652	0.80[ASN][1000 genomes]
rs3088080	0.84[JPT][hapmap]
rs36018423	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813133	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4814229	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814231	0.85[ASN][1000 genomes]
rs4814237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814243	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs4814244	0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs5019244	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033691	0.85[ASN][1000 genomes]
rs6033697	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033698	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033707	0.85[ASN][1000 genomes]
rs6033709	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033710	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033728	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033729	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033732	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033744	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033753	0.89[ASN][1000 genomes]
rs6033807	0.84[JPT][hapmap]
rs6042066	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042071	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042072	0.85[ASN][1000 genomes]
rs6042074	0.85[ASN][1000 genomes]
rs6042088	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042091	0.85[ASN][1000 genomes]
rs6042117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042131	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042160	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042170	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042172	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042175	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042197	0.84[ASN][1000 genomes]
rs6042208	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042209	0.84[ASN][1000 genomes]
rs6042238	0.80[ASN][1000 genomes]
rs6042270	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042283	0.80[ASN][1000 genomes]
rs6074593	0.85[ASN][1000 genomes]
rs6074623	0.93[ASN][1000 genomes]
rs6079009	0.85[ASN][1000 genomes]
rs6079010	0.85[ASN][1000 genomes]
rs6079012	0.85[ASN][1000 genomes]
rs6079013	0.85[ASN][1000 genomes]
rs6079015	0.85[ASN][1000 genomes]
rs6079133	0.83[JPT][hapmap]
rs6105079	0.85[ASN][1000 genomes]
rs6105081	0.85[ASN][1000 genomes]
rs6105102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105110	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6105165	0.84[JPT][hapmap]
rs6109825	0.85[ASN][1000 genomes]
rs6109893	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109894	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109912	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131468	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134916	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514382	0.85[ASN][1000 genomes]
rs6514383	0.85[ASN][1000 genomes]
rs6891	0.84[JPT][hapmap]
rs750424	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124053	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873523	0.84[ASN][1000 genomes]
rs910619	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs926977	0.89[ASN][1000 genomes]
rs932524	0.84[JPT][hapmap]
rs9575	0.84[JPT][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6042207	NSFL1C	cis	Brain Pons	GTEx
rs6042207	NSFL1C	cis	Frontal Cortex	GTEx
rs6042207	NSFL1C	cis	Temporal Cortex	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr20:1400000-1410600	Weak transcription	Osteobl	bone
4	chr20:1403200-1406200	Enhancers	NHEK	skin
5	chr20:1403200-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:1404000-1409000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr20:1404600-1407200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
9	chr20:1404800-1407000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:1404800-1407800	Weak transcription	Primary T cells from cord blood	blood
11	chr20:1404800-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:1404800-1408200	Weak transcription	Fetal Intestine Large	intestine
13	chr20:1404800-1408200	Weak transcription	Lung	lung
14	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
15	chr20:1405000-1406600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr20:1405000-1406800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr20:1405000-1407000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:1405000-1407200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:1405000-1407800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr20:1405000-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr20:1405000-1408200	Weak transcription	Adipose Nuclei	Adipose
22	chr20:1405000-1409600	Weak transcription	Stomach Mucosa	stomach
23	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
24	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr20:1405200-1407000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr20:1405200-1407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr20:1405200-1407800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:1405200-1408400	Weak transcription	K562	blood
29	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr20:1405400-1406600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr20:1405400-1406800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:1405400-1407200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:1405400-1407200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr20:1405400-1408000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
37	chr20:1405600-1408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:1405600-1409800	Weak transcription	HMEC	breast
39	chr20:1406000-1406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:1406000-1408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr20:1406000-1410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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