Variant report

Variant	rs8180538
Chromosome Location	chr6:56941361-56941362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56934363..56937473-chr6:56937699..56942406,5	K562	blood:
2	chr6:56934363..56937335-chr6:56939839..56941721,2	K562	blood:
3	chr6:56935225..56943628-chr6:56947006..56954759,13	K562	blood:

Variant related genes	Relation type
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1157713	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190416	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12192711	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12210597	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12211611	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1901382	0.83[EUR][1000 genomes]
rs2100305	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2273921	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734738	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778515	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800019	0.91[ASN][1000 genomes]
rs3996929	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3996933	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3996937	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4715646	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459180	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6913707	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6926980	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928715	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6929783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6936472	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743855	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7744316	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7744824	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753537	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753927	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7763570	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349843	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367704	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9367708	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370564	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370565	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382689	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396259	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952647	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9885757	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription 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
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1026524	chr6:56902544-56951703	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv885913	chr6:56910884-56954439	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv970684	chr6:56912349-56953340	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3374787	chr6:56912959-56955113	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	esv2763988	chr6:56913072-56952630	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv603189	chr6:56913453-56950609	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv538230	chr6:56913943-56951703	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv526143	chr6:56917538-56954439	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8180538	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs8180538	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56911800-56943000	Weak transcription	Esophagus	oesophagus
2	chr6:56913600-56941600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:56914600-56954200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:56916800-56954400	Weak transcription	Thymus	Thymus
5	chr6:56918400-56954200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:56925200-56941800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:56925400-56941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:56925400-56942200	Weak transcription	HSMMtube	muscle
9	chr6:56925400-56954400	Weak transcription	Primary B cells from cord blood	blood
10	chr6:56925600-56954200	Weak transcription	Hela-S3	cervix
11	chr6:56926400-56944600	Weak transcription	Pancreas	Pancrea
12	chr6:56926600-56954200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:56927000-56954800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:56927200-56954000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:56929200-56954200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:56929400-56954200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:56929800-56944800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:56930000-56941800	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:56930000-56943200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:56930000-56950000	Weak transcription	NHDF-Ad	bronchial
21	chr6:56930000-56954200	Weak transcription	Fetal Intestine Small	intestine
22	chr6:56930200-56944000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:56930200-56954000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:56930400-56944000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:56930400-56954200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:56930600-56946200	Weak transcription	HUVEC	blood vessel
27	chr6:56930600-56952800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:56931600-56954200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:56931800-56941400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:56931800-56942400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:56931800-56942800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:56931800-56943800	Weak transcription	HepG2	liver
33	chr6:56932400-56947200	Weak transcription	Adipose Nuclei	Adipose
34	chr6:56932600-56954200	Weak transcription	HMEC	breast
35	chr6:56933200-56954200	Weak transcription	HSMM	muscle
36	chr6:56933800-56947000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:56934200-56942800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:56934600-56947000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:56935200-56954200	Weak transcription	Placenta	Placenta
40	chr6:56935200-56954800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:56936400-56942200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:56937400-56952200	Weak transcription	K562	blood
43	chr6:56939000-56944600	Weak transcription	Fetal Stomach	stomach
44	chr6:56939000-56954400	Weak transcription	Ovary	ovary
45	chr6:56939200-56944600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:56939200-56944600	Weak transcription	Left Ventricle	heart
47	chr6:56939600-56954200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:56939600-56954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:56939600-56954400	Weak transcription	Aorta	Aorta
50	chr6:56939800-56941600	Weak transcription	GM12878-XiMat	blood

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