Variant report

Variant	rs6050535
Chromosome Location	chr20:25311544-25311545
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25290558..25292772-chr20:25309166..25311596,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 163 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1046073	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1077889	0.80[ASN][1000 genomes]
rs10966	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11100	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1130694	0.85[ASN][1000 genomes]
rs1888997	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1888998	0.83[ASN][1000 genomes]
rs1888999	0.83[ASN][1000 genomes]
rs2027003	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2027004	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2145126	0.80[ASN][1000 genomes]
rs2227890	0.80[ASN][1000 genomes]
rs2227892	0.80[ASN][1000 genomes]
rs2257233	0.80[ASN][1000 genomes]
rs2257420	0.85[ASN][1000 genomes]
rs2257432	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2257461	0.80[ASN][1000 genomes]
rs2257464	0.80[ASN][1000 genomes]
rs2257496	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2257705	0.80[ASN][1000 genomes]
rs2257712	0.80[ASN][1000 genomes]
rs2257808	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2257809	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2257982	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2257985	0.80[ASN][1000 genomes]
rs2257988	0.80[EUR][1000 genomes]
rs2257991	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2258066	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2258135	0.80[ASN][1000 genomes]
rs2258201	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2258563	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258617	0.80[EUR][1000 genomes]
rs2258719	0.83[ASN][1000 genomes]
rs2258728	0.85[ASN][1000 genomes]
rs2258769	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258879	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258884	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2259837	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2259873	0.81[ASN][1000 genomes]
rs2259926	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2259928	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2259956	0.85[ASN][1000 genomes]
rs2261109	0.80[ASN][1000 genomes]
rs2261115	0.80[ASN][1000 genomes]
rs2261698	0.80[ASN][1000 genomes]
rs2261720	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2261753	0.80[ASN][1000 genomes]
rs2261784	0.80[ASN][1000 genomes]
rs2261785	0.80[ASN][1000 genomes]
rs2261790	0.80[ASN][1000 genomes]
rs2261794	0.80[ASN][1000 genomes]
rs2297496	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297497	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424700	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2424704	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2424708	0.83[ASN][1000 genomes]
rs2424710	0.83[ASN][1000 genomes]
rs2424711	0.83[ASN][1000 genomes]
rs2474777	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2482919	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482923	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482927	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482928	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482930	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482931	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482932	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482937	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482940	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482941	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482948	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500399	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500400	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500401	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500404	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500405	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500432	0.83[ASN][1000 genomes]
rs2500433	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500443	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2500446	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2990512	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002698	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3002702	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs33999482	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34645895	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4355182	0.83[ASN][1000 genomes]
rs4813557	0.85[ASN][1000 genomes]
rs4813561	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813562	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813563	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815404	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815405	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815407	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815408	0.90[ASN][1000 genomes]
rs4815409	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815411	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815412	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815414	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6037083	0.85[ASN][1000 genomes]
rs6037085	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6037086	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6037095	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6037096	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6037097	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6037099	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050532	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050542	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6050544	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050547	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050555	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050556	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050559	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050561	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050562	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050563	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050564	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050565	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050566	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050567	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050573	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6076336	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6076339	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083799	0.82[ASN][1000 genomes]
rs6083801	0.90[ASN][1000 genomes]
rs6083804	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083805	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083809	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083813	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083817	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6083818	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083825	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083826	0.81[ASN][1000 genomes]
rs6107031	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6107033	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6115140	0.83[ASN][1000 genomes]
rs6115146	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6115153	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6115159	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66999585	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7019	0.83[ASN][1000 genomes]
rs7020	0.85[ASN][1000 genomes]
rs7267979	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7268053	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7343481	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113968	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8125868	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884613	0.83[ASN][1000 genomes]
rs910996	0.80[ASN][1000 genomes]
rs910997	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9927	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6050535	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6050535	PYGB	cis	Whole Blood	GTEx
rs6050535	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6050535	ABHD12	cis	Nerve Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292000-25325200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr20:25292000-25327400	Weak transcription	Aorta	Aorta
3	chr20:25292200-25316600	Weak transcription	NHEK	skin
4	chr20:25292400-25325200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
6	chr20:25296800-25316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:25297800-25317800	Weak transcription	Fetal Brain Female	brain
8	chr20:25302200-25317200	Weak transcription	Esophagus	oesophagus
9	chr20:25302800-25324400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:25304000-25324800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr20:25304400-25316800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:25304400-25317200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:25304400-25319000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr20:25304400-25324200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:25304400-25327000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr20:25304600-25317000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:25304600-25317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:25304800-25317800	Weak transcription	Gastric	stomach
19	chr20:25304800-25318000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr20:25304800-25322800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr20:25305000-25317200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:25305000-25327000	Weak transcription	Primary T cells from cord blood	blood
23	chr20:25305000-25331800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr20:25305400-25319000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr20:25305400-25319800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr20:25305400-25320400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr20:25305400-25320800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr20:25305400-25321000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr20:25305400-25321000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:25305400-25335000	Weak transcription	Primary B cells from cord blood	blood
31	chr20:25306200-25317000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr20:25306200-25317200	Weak transcription	Fetal Intestine Large	intestine
33	chr20:25306200-25317200	Weak transcription	Thymus	Thymus
34	chr20:25306200-25335800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr20:25306400-25316600	Weak transcription	Dnd41	blood
36	chr20:25306400-25321600	Weak transcription	Right Atrium	heart
37	chr20:25307200-25317800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr20:25307800-25318800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr20:25309400-25325600	Weak transcription	HSMM	muscle
40	chr20:25309600-25318600	Weak transcription	A549	lung
41	chr20:25309600-25321800	Weak transcription	Left Ventricle	heart
42	chr20:25309600-25333200	Weak transcription	NHLF	lung
43	chr20:25309800-25318200	Weak transcription	Right Ventricle	heart
44	chr20:25309800-25320200	Weak transcription	Colonic Mucosa	Colon
45	chr20:25309800-25320400	Weak transcription	Ovary	ovary
46	chr20:25309800-25323200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr20:25309800-25325000	Weak transcription	Brain Angular Gyrus	brain
48	chr20:25309800-25325400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr20:25310000-25317200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr20:25310000-25317400	Weak transcription	Spleen	Spleen

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