Variant report

Variant	rs6138639
Chromosome Location	chr20:25669052-25669053
allele	C/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	chr20:25668982-25669550	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:25668234-25669455	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25603881..25606612-chr20:25668010..25670254,2	K562	blood:
2	chr20:25603625..25606406-chr20:25665177..25670447,5	MCF-7	breast:

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

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11699872	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12480853	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2072977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs35016365	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35364051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59046052	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050690	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6050790	0.89[CHB][hapmap]
rs6115218	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6115241	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6132842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs6132851	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6132857	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132858	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6132861	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132862	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132863	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132864	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138595	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138604	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6138611	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138622	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138623	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138625	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138631	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138633	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138643	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6138647	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138650	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138651	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6138653	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138659	0.81[JPT][hapmap]
rs878176	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6138639	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138639	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138639	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138639	PYGB	cis	Whole Blood	GTEx
rs6138639	FAM182B	cis	Skin Sun Exposed Lower leg	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	chr20:25657600-25672200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:25657600-25672600	Weak transcription	Fetal Brain Male	brain
5	chr20:25657600-25676000	Weak transcription	Stomach Mucosa	stomach
6	chr20:25657600-25676200	Weak transcription	Hela-S3	cervix
7	chr20:25657600-25676200	Weak transcription	K562	blood
8	chr20:25657600-25676400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr20:25657800-25676000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr20:25657800-25676200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr20:25657800-25676200	Weak transcription	Colonic Mucosa	Colon
12	chr20:25657800-25676200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr20:25658200-25676200	Weak transcription	Fetal Kidney	kidney
14	chr20:25658400-25676200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr20:25658800-25676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:25659000-25676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr20:25660600-25676000	Weak transcription	HUVEC	blood vessel
18	chr20:25662200-25672000	Weak transcription	NH-A	brain
19	chr20:25662400-25676000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr20:25662600-25672200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr20:25662800-25672000	Weak transcription	Primary B cells from cord blood	blood
22	chr20:25663800-25676000	Weak transcription	HMEC	breast
23	chr20:25664000-25675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr20:25664000-25676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:25664000-25676000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:25664200-25672000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:25664200-25675200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr20:25664200-25676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr20:25666200-25672400	Weak transcription	HSMM	muscle
30	chr20:25666400-25676000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:25666400-25676400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr20:25666600-25671800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr20:25666800-25672200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr20:25666800-25672200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:25666800-25674200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr20:25666800-25676000	Weak transcription	Brain Substantia Nigra	brain
37	chr20:25666800-25676200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr20:25666800-25676400	Weak transcription	Ovary	ovary
39	chr20:25667000-25671000	Weak transcription	Left Ventricle	heart
40	chr20:25667000-25672000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr20:25667000-25672000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr20:25667000-25672000	Weak transcription	NHLF	lung
43	chr20:25667000-25672200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr20:25667000-25672200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr20:25667000-25672200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr20:25667000-25672200	Weak transcription	Fetal Lung	lung
47	chr20:25667000-25672600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr20:25667000-25672800	Weak transcription	GM12878-XiMat	blood
49	chr20:25667000-25675200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr20:25667000-25675400	Weak transcription	Brain Cingulate Gyrus	brain

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