Variant report

Variant	rs3829698
Chromosome Location	chr20:1430550-1430551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1429690..1432068-chr20:1446953..1449118,3	K562	blood:
2	chr20:1429669..1432038-chr20:1440054..1444992,4	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1028508	0.92[ASN][1000 genomes]
rs11699735	0.93[ASN][1000 genomes]
rs13063	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs1884389	0.82[CHD][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap]
rs1884391	0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs2144544	0.88[ASN][1000 genomes]
rs2144545	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2144546	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs2317513	0.86[ASN][1000 genomes]
rs2317652	0.92[ASN][1000 genomes]
rs3088080	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.93[ASN][1000 genomes]
rs3171292	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs3210915	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs3795135	0.86[CHB][hapmap]
rs4352285	0.92[CHB][hapmap];0.82[CHD][hapmap];0.89[ASN][1000 genomes]
rs4546067	0.92[CHB][hapmap];0.82[CHD][hapmap];0.89[ASN][1000 genomes]
rs4813133	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs4814243	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6033807	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6042238	0.92[ASN][1000 genomes]
rs6042244	0.84[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs6042268	0.88[ASN][1000 genomes]
rs6042270	0.92[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042283	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6042292	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs6042354	0.92[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs6079133	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs6079138	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6079139	0.89[ASN][1000 genomes]
rs6105110	0.88[JPT][hapmap]
rs6105165	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs6131506	0.93[ASN][1000 genomes]
rs6891	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.93[ASN][1000 genomes]
rs910619	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs910620	0.92[CHB][hapmap];0.87[CHD][hapmap];0.89[ASN][1000 genomes]
rs932524	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs9575	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[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
rs3829698	NSFL1C	cis	lymphoblastoid	seeQTL
rs3829698	NSFL1C	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1419000-1430600	Strong transcription	Fetal Stomach	stomach
2	chr20:1419000-1431400	Strong transcription	Brain Germinal Matrix	brain
3	chr20:1419000-1431800	Strong transcription	Brain Hippocampus Middle	brain
4	chr20:1419200-1431800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr20:1419200-1443400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr20:1419600-1431000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr20:1419600-1432000	Strong transcription	Fetal Intestine Large	intestine
8	chr20:1419600-1442000	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr20:1419800-1443600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr20:1420000-1431400	Strong transcription	Fetal Brain Female	brain
11	chr20:1420000-1431600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr20:1420000-1431600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr20:1420000-1431800	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr20:1420000-1431800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:1420000-1432000	Strong transcription	Liver	Liver
16	chr20:1420200-1430600	Strong transcription	Fetal Intestine Small	intestine
17	chr20:1420200-1430600	Strong transcription	Pancreas	Pancrea
18	chr20:1420200-1430600	Strong transcription	Right Ventricle	heart
19	chr20:1420200-1431200	Strong transcription	Primary B cells from cord blood	blood
20	chr20:1420200-1431400	Strong transcription	Left Ventricle	heart
21	chr20:1420200-1431600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:1420200-1431800	Strong transcription	Adipose Nuclei	Adipose
23	chr20:1420200-1431800	Strong transcription	Ovary	ovary
24	chr20:1420200-1437200	Strong transcription	Rectal Smooth Muscle	rectum
25	chr20:1420200-1444000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:1420200-1445600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr20:1420400-1430600	Strong transcription	Aorta	Aorta
28	chr20:1420400-1430600	Strong transcription	Spleen	Spleen
29	chr20:1420400-1430800	Strong transcription	Brain Angular Gyrus	brain
30	chr20:1420400-1430800	Strong transcription	Gastric	stomach
31	chr20:1420400-1431200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:1420400-1431800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:1420400-1431800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr20:1420400-1443600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr20:1420400-1444600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr20:1420400-1444800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:1420400-1445800	Strong transcription	A549	lung
38	chr20:1420600-1431400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:1420600-1431800	Strong transcription	Brain Substantia Nigra	brain
40	chr20:1420600-1431800	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr20:1420600-1444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr20:1420800-1430600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr20:1421000-1431000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:1421000-1431800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:1421200-1430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr20:1421200-1444400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr20:1421400-1445200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr20:1421400-1446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr20:1421600-1431200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr20:1421600-1431400	Strong transcription	Dnd41	blood

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