Variant report

Variant	rs6138595
Chromosome Location	chr20:25509632-25509633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25371156..25372734-chr20:25509417..25511739,2	MCF-7	breast:
2	chr20:25504894..25507358-chr20:25508312..25510600,2	MCF-7	breast:
3	chr20:25508566..25510611-chr20:25564676..25566360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11699872	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12480853	0.83[JPT][hapmap]
rs2072975	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2072977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2235605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2235606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2235607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261177	0.84[AMR][1000 genomes]
rs2263205	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs2294583	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2482933	0.83[AMR][1000 genomes]
rs2482934	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs2482947	0.84[AMR][1000 genomes]
rs2500403	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs2500441	0.84[AMR][1000 genomes]
rs35016365	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35364051	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59046052	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6050690	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6050790	0.83[CHB][hapmap]
rs6115218	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs6115241	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6132842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132851	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6132857	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132858	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132861	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132862	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132863	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138569	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6138573	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6138576	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6138580	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138584	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138601	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138604	0.93[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6138611	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138622	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138623	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138625	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138631	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138633	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138639	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138643	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138647	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138650	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138651	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs723774	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs878176	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription 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
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv979406	chr20:25509600-25513942	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6138595	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6138595	PYGB	cis	Whole Blood	GTEx
rs6138595	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138595	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138595	ABHD12	cis	lymphoblastoid	seeQTL
rs6138595	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138595	NINL	cis	cerebellum	SCAN
rs6138595	NINL	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
5	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
6	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
10	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr20:25498000-25511000	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:25498200-25510800	Weak transcription	Brain Substantia Nigra	brain
13	chr20:25498200-25512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25498200-25512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
17	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
18	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
19	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
20	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr20:25498200-25519400	Weak transcription	Gastric	stomach
22	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
26	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25503400-25512400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr20:25504800-25512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr20:25505000-25512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:25505200-25512800	Weak transcription	Esophagus	oesophagus
31	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
32	chr20:25505400-25513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:25505400-25514600	Weak transcription	Lung	lung
34	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:25507000-25510600	Weak transcription	Fetal Brain Male	brain
36	chr20:25507000-25512800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr20:25507200-25510800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr20:25507200-25512200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:25507200-25512400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr20:25507200-25512600	Weak transcription	Fetal Muscle Leg	muscle
41	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
42	chr20:25507400-25510600	Weak transcription	Fetal Brain Female	brain
43	chr20:25507400-25510800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr20:25507400-25512200	Weak transcription	Thymus	Thymus
45	chr20:25507400-25512200	Weak transcription	Spleen	Spleen
46	chr20:25507400-25512400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25507400-25512400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr20:25507400-25512600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr20:25507400-25512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr20:25507400-25512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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