Variant report

Variant	rs12194288
Chromosome Location	chr6:57063491-57063492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57062290..57064977-chr6:57069550..57072022,3	MCF-7	breast:
2	chr6:57036970..57039600-chr6:57062053..57063901,3	MCF-7	breast:
3	chr6:57062077..57064175-chr6:57065687..57067703,2	K562	blood:

Variant related genes	Relation type
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1020550	0.80[ASN][1000 genomes]
rs10484410	0.90[ASN][1000 genomes]
rs11398	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190575	0.90[ASN][1000 genomes]
rs12192222	0.90[ASN][1000 genomes]
rs12194407	0.90[ASN][1000 genomes]
rs12198801	0.90[ASN][1000 genomes]
rs12201039	1.00[ASN][1000 genomes]
rs12211901	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214882	0.90[ASN][1000 genomes]
rs1411578	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547226	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs16888392	1.00[ASN][1000 genomes]
rs17619360	0.90[ASN][1000 genomes]
rs3800018	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3800023	0.90[ASN][1000 genomes]
rs3800025	0.80[ASN][1000 genomes]
rs3996934	0.80[ASN][1000 genomes]
rs3996935	0.80[ASN][1000 genomes]
rs3996936	0.80[ASN][1000 genomes]
rs4523090	0.80[ASN][1000 genomes]
rs4631287	0.80[ASN][1000 genomes]
rs6459178	0.90[ASN][1000 genomes]
rs6936506	0.90[ASN][1000 genomes]
rs72868608	1.00[ASN][1000 genomes]
rs7744148	0.80[ASN][1000 genomes]
rs7748120	0.80[ASN][1000 genomes]
rs7748453	0.80[ASN][1000 genomes]
rs7753547	0.80[ASN][1000 genomes]
rs7764446	0.80[ASN][1000 genomes]
rs7771115	0.90[ASN][1000 genomes]
rs9396256	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12194288	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs12194288	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:57038200-57063800	Weak transcription	Esophagus	oesophagus
3	chr6:57038200-57063800	Weak transcription	Gastric	stomach
4	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
5	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
6	chr6:57038600-57064000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
8	chr6:57039600-57064000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:57042200-57064000	Weak transcription	Colonic Mucosa	Colon
10	chr6:57043800-57063800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:57048200-57064200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:57048200-57072200	Weak transcription	Fetal Brain Male	brain
13	chr6:57048400-57067200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:57048400-57067200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:57048800-57063800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:57049000-57072600	Weak transcription	Psoas Muscle	Psoas
17	chr6:57049400-57063600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:57049400-57063800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:57049400-57063800	Weak transcription	Lung	lung
20	chr6:57049400-57085000	Weak transcription	Aorta	Aorta
21	chr6:57050800-57072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:57051000-57063800	Weak transcription	Left Ventricle	heart
23	chr6:57054400-57063800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:57054400-57067000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:57055600-57063600	Weak transcription	HepG2	liver
26	chr6:57055600-57063800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:57056200-57063800	Weak transcription	A549	lung
28	chr6:57056600-57086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:57056800-57063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:57056800-57064000	Weak transcription	HSMMtube	muscle
31	chr6:57057000-57067800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:57057200-57063800	Weak transcription	NHLF	lung
33	chr6:57057200-57065200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:57057200-57067000	Weak transcription	Fetal Kidney	kidney
35	chr6:57057200-57081200	Weak transcription	HMEC	breast
36	chr6:57057600-57063800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:57057600-57063800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:57057600-57081200	Weak transcription	Fetal Intestine Small	intestine
39	chr6:57057800-57071400	Weak transcription	Fetal Thymus	thymus
40	chr6:57058000-57063600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:57058000-57063800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:57058000-57066600	Weak transcription	Fetal Intestine Large	intestine
43	chr6:57058000-57074200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:57058000-57080800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:57058200-57063600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:57058200-57063800	Weak transcription	Placenta	Placenta
47	chr6:57058200-57066400	Weak transcription	Primary T cells from cord blood	blood
48	chr6:57058200-57072800	Weak transcription	K562	blood
49	chr6:57058200-57079200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:57058200-57085800	Weak transcription	Fetal Muscle Leg	muscle

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