Variant report

Variant	rs2317651
Chromosome Location	chr20:1414025-1414026
allele	C/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:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1028508	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11699735	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13063	0.80[ASN][1000 genomes]
rs1884389	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1884391	0.81[ASN][1000 genomes]
rs2144544	0.81[ASN][1000 genomes]
rs2144545	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2317652	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3088080	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3171292	0.80[ASN][1000 genomes]
rs3210915	0.80[ASN][1000 genomes]
rs4352285	0.80[ASN][1000 genomes]
rs4546067	0.80[ASN][1000 genomes]
rs6033807	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042238	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042244	0.81[ASN][1000 genomes]
rs6042268	0.81[ASN][1000 genomes]
rs6042270	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042283	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042292	0.80[ASN][1000 genomes]
rs6079133	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6079138	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6079139	0.80[ASN][1000 genomes]
rs6105165	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6131506	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6131519	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6891	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs910619	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910620	0.80[ASN][1000 genomes]
rs932524	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9575	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2317651	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
3	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
4	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
5	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
9	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
10	chr20:1408600-1414400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
12	chr20:1408800-1414200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:1408800-1414400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:1408800-1415000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
23	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
24	chr20:1410200-1415000	Weak transcription	HMEC	breast
25	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
26	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr20:1410800-1414600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr20:1411000-1414600	Weak transcription	K562	blood
29	chr20:1411000-1415000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:1411000-1415000	Weak transcription	Adipose Nuclei	Adipose
31	chr20:1411000-1415200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:1411000-1415200	Weak transcription	NHEK	skin
33	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
34	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
35	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:1411400-1415000	Weak transcription	Osteobl	bone
39	chr20:1411400-1415200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:1411400-1415200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr20:1411600-1415000	Weak transcription	NHDF-Ad	bronchial
42	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
43	chr20:1412000-1415000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:1412000-1415200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr20:1412200-1414400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr20:1412400-1414200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr20:1412400-1414200	Weak transcription	A549	lung
48	chr20:1412400-1419000	Weak transcription	Brain Hippocampus Middle	brain
49	chr20:1412600-1414400	Weak transcription	Dnd41	blood
50	chr20:1412800-1415400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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