Variant report

Variant	rs4078165
Chromosome Location	chr18:6730946-6730947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr18:6730632-6731685	MCF10A-Er-Src	breast:	n/a	chr18:6731481-6731496
2	TCF7L2	chr18:6730454-6731918	HEK293	kidney:	n/a	chr18:6731012-6731022
3	STAT3	chr18:6730859-6731776	MCF10A-Er-Src	breast:	n/a	chr18:6731380-6731391

No.	Distal block	Cell Line	Cell type
1	chr18:6725447..6727785-chr18:6730502..6732481,2	K562	blood:
2	chr18:6725183..6727933-chr18:6730767..6732565,3	K562	blood:
3	chr18:6715232..6717469-chr18:6730082..6731975,2	K562	blood:

Variant related genes	Relation type
ENSG00000266441	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11081264	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11660237	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11661838	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11663135	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150787	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326891	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12455302	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381520	0.82[ASN][1000 genomes]
rs13381524	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28463953	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132206	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797256	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4798487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55866900	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56061391	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62081458	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230965	0.80[ASN][1000 genomes]
rs7231122	0.80[ASN][1000 genomes]
rs7237200	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505315	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7505419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675928	0.81[ASN][1000 genomes]
rs9946622	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059678	chr18:6155114-6838290	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1055148	chr18:6527292-6790869	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv543629	chr18:6527292-6790869	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3529901	chr18:6537233-6851509	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3529902	chr18:6537233-6851509	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1057885	chr18:6598684-6754548	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking 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	25 gene(s)	inside rSNPs	diseases
12	esv3417418	chr18:6729302-6731400	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4078165	ARHGAP28	cis	Thyroid	GTEx
rs4078165	RP11-91I8.3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6729000-6731200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:6729000-6731200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:6729000-6731400	Active TSS	Fetal Intestine Large	intestine
4	chr18:6729000-6731400	Active TSS	Fetal Lung	lung
5	chr18:6729000-6731400	Active TSS	Ovary	ovary
6	chr18:6729000-6731400	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr18:6729000-6731600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr18:6729000-6731600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr18:6729000-6731800	Active TSS	Brain Germinal Matrix	brain
10	chr18:6729200-6731000	Active TSS	Fetal Stomach	stomach
11	chr18:6729200-6731400	Active TSS	HSMM	muscle
12	chr18:6729200-6731600	Active TSS	Colonic Mucosa	Colon
13	chr18:6729400-6731200	Active TSS	Fetal Muscle Leg	muscle
14	chr18:6729400-6731400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr18:6730000-6732000	ZNF genes & repeats	Fetal Brain Male	brain
16	chr18:6730200-6731400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:6730200-6731400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:6730200-6731400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:6730200-6731400	Weak transcription	Gastric	stomach
20	chr18:6730200-6731400	Weak transcription	Pancreas	Pancrea
21	chr18:6730200-6731600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr18:6730200-6731800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr18:6730200-6731800	Flanking Active TSS	Osteobl	bone
24	chr18:6730200-6735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr18:6730200-6747800	Weak transcription	Left Ventricle	heart
26	chr18:6730400-6731200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr18:6730400-6731200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr18:6730400-6731200	Flanking Active TSS	Fetal Heart	heart
29	chr18:6730400-6731400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr18:6730400-6731400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr18:6730400-6731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr18:6730400-6731400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr18:6730400-6731600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr18:6730400-6731600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr18:6730400-6731800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr18:6730400-6731800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:6730400-6731800	Flanking Active TSS	HSMMtube	muscle
38	chr18:6730400-6731800	Flanking Active TSS	HUVEC	blood vessel
39	chr18:6730400-6732000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:6730400-6732200	Enhancers	Hela-S3	cervix
41	chr18:6730400-6735600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr18:6730600-6731200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:6730600-6731200	Active TSS	Duodenum Mucosa	Duodenum
44	chr18:6730600-6731200	Weak transcription	NHEK	skin
45	chr18:6730600-6731400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr18:6730600-6731400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr18:6730600-6731600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:6730600-6731600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr18:6730600-6731800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr18:6730600-6731800	Enhancers	Colon Smooth Muscle	Colon

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