Variant report

Variant	rs7239808
Chromosome Location	chr18:6728678-6728679
allele	A/T
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	POLR2A	chr18:6728653-6730345	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr18:6728508-6730205	K562	blood:	n/a	chr18:6728931-6728940
3	IRF1	chr18:6728419-6729443	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
4	ARID3A	chr18:6728394-6729188	K562	blood:	n/a	n/a
5	EP300	chr18:6728506-6730047	K562	blood:	n/a	chr18:6728958-6728968 chr18:6729195-6729209 chr18:6729184-6729198 chr18:6729101-6729114 chr18:6729692-6729708 chr18:6729725-6729741 chr18:6729297-6729310 chr18:6728929-6728938 chr18:6729793-6729802
6	IRF1	chr18:6728650-6729923	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
7	TBL1XR1	chr18:6728649-6729149	K562	blood:	n/a	n/a
8	RCOR1	chr18:6728258-6730223	K562	blood:	n/a	n/a
9	MYC	chr18:6728264-6730163	K562	blood:	n/a	chr18:6729601-6729611 chr18:6728555-6728564
10	IRF1	chr18:6728671-6729906	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
11	MAZ	chr18:6728437-6730186	K562	blood:	n/a	chr18:6729601-6729611 chr18:6728555-6728564

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:6711773..6713499-chr18:6727376..6728976,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP28-6	chr18:6727002-6728980	NONHSAT057118

Variant related genes	Relation type
ARHGAP28	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10853339	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081256	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081258	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11081261	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081262	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081263	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081265	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663818	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11663883	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11876610	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456109	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12458536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12458555	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605298	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956941	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12962460	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381520	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28402892	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28675797	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34146208	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35451382	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4078265	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4605246	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798486	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4798489	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55847427	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57509765	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6417043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506429	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506430	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506431	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506438	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506439	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7227172	0.84[EUR][1000 genomes]
rs7227965	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7228459	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7232028	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232807	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233410	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235385	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237087	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237204	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7238175	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7240348	0.83[EUR][1000 genomes]
rs7242667	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880705	0.85[EUR][1000 genomes]
rs7504466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506354	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506610	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7506974	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8084747	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8088863	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093374	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952482	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7239808	RP11-91I8.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6717200-6728800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:6721000-6729000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr18:6723200-6728800	Weak transcription	Fetal Stomach	stomach
4	chr18:6725000-6728800	Weak transcription	Placenta	Placenta
5	chr18:6725200-6728800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr18:6725200-6728800	Weak transcription	Adipose Nuclei	Adipose
7	chr18:6725200-6728800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr18:6725200-6729000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr18:6727400-6728800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:6727400-6728800	Weak transcription	Gastric	stomach
11	chr18:6727400-6728800	Weak transcription	HSMMtube	muscle
12	chr18:6727600-6728800	Weak transcription	Brain Germinal Matrix	brain
13	chr18:6727600-6728800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr18:6728200-6729000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:6728400-6728800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:6728400-6728800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr18:6728400-6728800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:6728400-6728800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr18:6728400-6728800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:6728400-6728800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr18:6728400-6728800	Enhancers	Fetal Intestine Small	intestine
22	chr18:6728400-6728800	Enhancers	Fetal Muscle Leg	muscle
23	chr18:6728400-6728800	Enhancers	HUVEC	blood vessel
24	chr18:6728400-6729000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr18:6728400-6729000	Flanking Active TSS	Fetal Kidney	kidney
26	chr18:6728400-6729000	Flanking Active TSS	Fetal Lung	lung
27	chr18:6728400-6729000	Bivalent Enhancer	NHDF-Ad	bronchial
28	chr18:6728400-6729200	Flanking Active TSS	K562	blood
29	chr18:6728400-6730600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:6728600-6728800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr18:6728600-6728800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:6728600-6728800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:6728600-6729000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr18:6728600-6729000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
35	chr18:6728600-6729000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr18:6728600-6729000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr18:6728600-6729000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr18:6728600-6729000	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr18:6728600-6729000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr18:6728600-6729200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr18:6728600-6729200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr18:6728600-6729200	Flanking Active TSS	HSMM	muscle
43	chr18:6728600-6729200	Flanking Active TSS	NH-A	brain
44	chr18:6728600-6729400	Enhancers	Fetal Heart	heart
45	chr18:6728600-6730600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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