Variant report

Variant	rs6042270
Chromosome Location	chr20:1416182-1416183
allele	A/C
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	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
3	chr20:1396270..1398331-chr20:1415556..1418372,2	K562	blood:
4	chr20:1405728..1407229-chr20:1414214..1416774,2	MCF-7	breast:
5	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: 6 )

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

rs_ID	r²[population]
rs1028508	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11087052	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs11699735	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063	0.83[CHB][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];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884391	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]
rs2144545	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]
rs2144546	0.92[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2317513	0.92[ASN][1000 genomes]
rs2317651	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2317652	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088080	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3171292	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3210915	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs36018423	0.80[ASN][1000 genomes]
rs3795135	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3829698	0.92[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs4352285	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4546067	0.83[CHB][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	0.84[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	0.85[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]
rs6042117	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042118	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	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042244	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6042268	0.96[ASN][1000 genomes]
rs6042283	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042292	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042354	0.83[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6074631	0.84[ASN][1000 genomes]
rs6079133	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079138	0.88[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	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.91[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	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131519	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6134916	0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs6891	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs750424	0.80[ASN][1000 genomes]
rs8124053	0.89[JPT][hapmap]
rs910619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910620	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs932524	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9575	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6042270	NSFL1C	cis	Frontal Cortex	GTEx
rs6042270	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs6042270	NSFL1C	cis	Temporal Cortex	GTEx
rs6042270	NSFL1C	cis	Cerebellum	GTEx
rs6042270	NSFL1C	cis	multi-tissue	Pritchard
rs6042270	NSFL1C	cis	Brain Pons	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
5	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
6	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
7	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
14	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
15	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
16	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
18	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
19	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
23	chr20:1412400-1419000	Weak transcription	Brain Hippocampus Middle	brain
24	chr20:1412800-1420200	Weak transcription	Ovary	ovary
25	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
26	chr20:1413800-1419200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr20:1413800-1420400	Weak transcription	Gastric	stomach
28	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
29	chr20:1414400-1416200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:1414400-1416800	Enhancers	Primary hematopoietic stem cells	blood
31	chr20:1414400-1416800	Enhancers	Dnd41	blood
32	chr20:1414600-1416200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr20:1414600-1416200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr20:1414600-1416400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr20:1414600-1416400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr20:1414600-1416400	Enhancers	Fetal Thymus	thymus
37	chr20:1414600-1416800	Enhancers	Primary B cells from peripheral blood	blood
38	chr20:1414600-1416800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr20:1414600-1419600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:1414800-1416800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr20:1414800-1419000	Weak transcription	Fetal Stomach	stomach
42	chr20:1415000-1416200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:1415000-1416200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr20:1415000-1416200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr20:1415000-1416200	Enhancers	HMEC	breast
46	chr20:1415000-1416200	Enhancers	HSMMtube	muscle
47	chr20:1415000-1416200	Enhancers	NHLF	lung
48	chr20:1415000-1416400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr20:1415000-1416600	Enhancers	Primary T cells from cord blood	blood
50	chr20:1415000-1416600	Enhancers	Primary T helper cells PMA-I stimulated	--

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