Variant report

Variant	rs6050790
Chromosome Location	chr20:25672341-25672342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25672136-25672527	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr20:25672339-25672574	K562	blood:	n/a	n/a
3	POLR2A	chr20:25671975-25672801	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25671071..25673125-chr20:25675586..25678423,3	K562	blood:
2	chr20:25603480..25606369-chr20:25672275..25675110,4	MCF-7	breast:
3	chr20:25671071..25673125-chr20:25675873..25678423,2	K562	blood:

Variant related genes	Relation type
ZNF337	TF binding region
ENSG00000213742	Chromatin interaction
ENSG00000130684	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs35364051	0.89[CHB][hapmap]
rs6115218	0.89[CHB][hapmap]
rs6115241	0.84[CHB][hapmap]
rs6132842	0.89[CHB][hapmap]
rs6138595	0.83[CHB][hapmap]
rs6138598	0.89[CHB][hapmap]
rs6138599	0.89[CHB][hapmap]
rs6138601	0.89[CHB][hapmap]
rs6138616	0.89[CHB][hapmap]
rs6138639	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6050790	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6050790	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6050790	PYGB	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25657200-25674200	Weak transcription	Fetal Heart	heart
2	chr20:25657400-25676200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr20:25657600-25672600	Weak transcription	Fetal Brain Male	brain
4	chr20:25657600-25676000	Weak transcription	Stomach Mucosa	stomach
5	chr20:25657600-25676200	Weak transcription	Hela-S3	cervix
6	chr20:25657600-25676200	Weak transcription	K562	blood
7	chr20:25657600-25676400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:25657800-25676000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr20:25657800-25676200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr20:25657800-25676200	Weak transcription	Colonic Mucosa	Colon
11	chr20:25657800-25676200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:25658200-25676200	Weak transcription	Fetal Kidney	kidney
13	chr20:25658400-25676200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:25658800-25676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr20:25659000-25676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr20:25660600-25676000	Weak transcription	HUVEC	blood vessel
17	chr20:25662400-25676000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr20:25663800-25676000	Weak transcription	HMEC	breast
19	chr20:25664000-25675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr20:25664000-25676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:25664000-25676000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr20:25664200-25675200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr20:25664200-25676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr20:25666200-25672400	Weak transcription	HSMM	muscle
25	chr20:25666400-25676000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr20:25666400-25676400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr20:25666800-25674200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr20:25666800-25676000	Weak transcription	Brain Substantia Nigra	brain
29	chr20:25666800-25676200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr20:25666800-25676400	Weak transcription	Ovary	ovary
31	chr20:25667000-25672600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr20:25667000-25672800	Weak transcription	GM12878-XiMat	blood
33	chr20:25667000-25675200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr20:25667000-25675400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:25667000-25676000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr20:25667000-25676000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr20:25667000-25676000	Weak transcription	Spleen	Spleen
38	chr20:25667000-25676000	Weak transcription	NHEK	skin
39	chr20:25667000-25676200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr20:25667000-25676200	Weak transcription	Liver	Liver
41	chr20:25667000-25676200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr20:25667200-25672400	Weak transcription	Placenta	Placenta
43	chr20:25667200-25672800	Weak transcription	Fetal Brain Female	brain
44	chr20:25667200-25674000	Weak transcription	Lung	lung
45	chr20:25667200-25675400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:25667200-25675400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr20:25667200-25675400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr20:25667200-25675600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr20:25667200-25676000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr20:25667200-25676000	Weak transcription	Colon Smooth Muscle	Colon

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