Variant report

Variant	rs1411578
Chromosome Location	chr6:57054843-57054844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57054194..57055111-chr6:57181143..57181875,2	K562	blood:
2	chr6:57054645..57055602-chr6:57180976..57181857,8	MCF-7	breast:
3	chr6:57054690..57057320-chr6:57086492..57088498,2	MCF-7	breast:
4	chr6:57038874..57041338-chr6:57054270..57057201,3	K562	blood:
5	chr6:57052066..57056020-chr6:57057599..57062110,6	K562	blood:
6	chr6:57054788..57055522-chr6:57132728..57133505,2	K562	blood:
7	chr6:57054267..57055185-chr6:57188775..57189678,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226803	Chromatin interaction
ENSG00000112210	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1020550	0.80[ASN][1000 genomes]
rs10484410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11398	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190575	0.90[ASN][1000 genomes]
rs12192222	0.90[ASN][1000 genomes]
rs12194288	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194407	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12198801	0.90[ASN][1000 genomes]
rs12201039	1.00[ASN][1000 genomes]
rs12211901	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16888392	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17619360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3800023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6936506	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72868608	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7753547	0.80[ASN][1000 genomes]
rs7756421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7771115	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1411578	RAB23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57056000	Weak transcription	Spleen	Spleen
2	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:57038200-57063800	Weak transcription	Esophagus	oesophagus
4	chr6:57038200-57063800	Weak transcription	Gastric	stomach
5	chr6:57038400-57056200	Weak transcription	Brain Germinal Matrix	brain
6	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
7	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
8	chr6:57038600-57064000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:57038800-57056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:57038800-57060400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:57039000-57056400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
13	chr6:57039200-57056200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:57039400-57056200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:57039600-57064000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:57042200-57064000	Weak transcription	Colonic Mucosa	Colon
17	chr6:57042800-57060400	Weak transcription	Right Ventricle	heart
18	chr6:57043800-57063800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:57044000-57056200	Strong transcription	A549	lung
20	chr6:57044000-57057600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:57044400-57059000	Strong transcription	Osteobl	bone
22	chr6:57045400-57055600	Weak transcription	Fetal Heart	heart
23	chr6:57045600-57059400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:57046800-57058800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:57048000-57056200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:57048000-57059000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:57048200-57056000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:57048200-57056200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:57048200-57064200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:57048200-57072200	Weak transcription	Fetal Brain Male	brain
31	chr6:57048400-57057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:57048400-57059800	Weak transcription	Primary B cells from cord blood	blood
33	chr6:57048400-57067200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:57048400-57067200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:57048800-57056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:57048800-57058200	Weak transcription	HUVEC	blood vessel
37	chr6:57048800-57060400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:57048800-57063800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:57049000-57056400	Weak transcription	Fetal Intestine Large	intestine
40	chr6:57049000-57072600	Weak transcription	Psoas Muscle	Psoas
41	chr6:57049400-57055800	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:57049400-57056200	Weak transcription	Fetal Stomach	stomach
43	chr6:57049400-57057800	Weak transcription	Adipose Nuclei	Adipose
44	chr6:57049400-57058400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:57049400-57059400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:57049400-57063600	Weak transcription	Brain Anterior Caudate	brain
47	chr6:57049400-57063800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:57049400-57063800	Weak transcription	Lung	lung
49	chr6:57049400-57085000	Weak transcription	Aorta	Aorta
50	chr6:57049600-57057000	Weak transcription	Hela-S3	cervix

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