Variant report

Variant	rs7506354
Chromosome Location	chr18:6728903-6728904
allele	C/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	REST	chr18:6728701-6730477	H1-neurons	neurons:	n/a	chr18:6729715-6729728 chr18:6729711-6729731
2	E2F6	chr18:6728839-6730248	K562	blood:	n/a	chr18:6729600-6729609 chr18:6729725-6729734
3	POLR2A	chr18:6728885-6730175	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF263	chr18:6728746-6730123	HEK293-T-REx	kidney:	n/a	chr18:6728824-6728833
5	ZNF384	chr18:6728819-6730093	K562	blood:	n/a	n/a
6	MAZ	chr18:6728769-6730272	IMR90	lung:	n/a	chr18:6729601-6729611
7	POLR2A	chr18:6728653-6730345	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr18:6728829-6730163	K562	blood:	n/a	n/a
9	CTCF	chr18:6728740-6729391	K562	blood:	n/a	chr18:6729229-6729242
10	HMGN3	chr18:6728713-6730134	K562	blood:	n/a	n/a
11	JUND	chr18:6728508-6730205	K562	blood:	n/a	chr18:6728931-6728940
12	IRF1	chr18:6728419-6729443	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
13	MAZ	chr18:6728890-6730131	Hela-S3	cervix:	n/a	chr18:6729601-6729611
14	ARID3A	chr18:6728394-6729188	K562	blood:	n/a	n/a
15	POLR2A	chr18:6728839-6730114	K562	blood:	n/a	n/a
16	POLR2A	chr18:6728830-6729036	K562	blood:	n/a	n/a
17	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
18	TAF1	chr18:6728889-6730172	H1-hESC	embryonic stem cell:	n/a	n/a
19	MXI1	chr18:6728715-6730225	IMR90	lung:	n/a	n/a
20	POLR2A	chr18:6728733-6730187	K562	blood:	n/a	n/a
21	TBP	chr18:6728859-6730125	K562	blood:	n/a	n/a
22	MAX	chr18:6728854-6730217	K562	blood:	n/a	chr18:6729601-6729611
23	IRF1	chr18:6728650-6729923	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
24	TBL1XR1	chr18:6728649-6729149	K562	blood:	n/a	n/a
25	MAFK	chr18:6728829-6729145	K562	blood:	n/a	n/a
26	STAT1	chr18:6728832-6730170	Hela-S3	cervix:	n/a	chr18:6729268-6729279 chr18:6729119-6729127 chr18:6729267-6729281 chr18:6729170-6729182
27	POLR2A	chr18:6728842-6730280	K562	blood:	n/a	n/a
28	CCNT2	chr18:6728692-6730125	K562	blood:	n/a	n/a
29	POLR2A	chr18:6728873-6730328	SK-N-MC	brain:	n/a	n/a
30	RCOR1	chr18:6728843-6730168	K562	blood:	n/a	n/a
31	RCOR1	chr18:6728258-6730223	K562	blood:	n/a	n/a
32	MXI1	chr18:6728849-6730768	SK-N-SH	brain:	n/a	n/a
33	MYC	chr18:6728264-6730163	K562	blood:	n/a	chr18:6729601-6729611 chr18:6728555-6728564
34	IRF1	chr18:6728671-6729906	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
35	MYC	chr18:6728779-6730204	K562	blood:	n/a	chr18:6729601-6729611
36	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-LAMA1-3	chr18:6728833-6729167	XLOC_012748
2	lnc-LAMA1-3	chr18:6728820-6729167	ENSG00000266441.1
3	lnc-ARHGAP28-6	chr18:6727002-6728980	NONHSAT057118

Variant related genes	Relation type
ARHGAP28	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10853339	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081256	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081258	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11081261	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081262	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081263	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081265	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663818	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11663883	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11876610	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456109	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12458536	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12458555	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605298	0.80[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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381520	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28402892	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28675797	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34146208	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35451382	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4078265	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4605246	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798486	0.96[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	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57509765	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6417043	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506429	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506430	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506431	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506432	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506434	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506438	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506439	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7227172	0.84[EUR][1000 genomes]
rs7227965	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7228459	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7232028	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232807	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233049	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233410	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233739	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235385	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237087	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237204	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7238175	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239808	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240348	0.83[EUR][1000 genomes]
rs7242667	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880705	0.85[EUR][1000 genomes]
rs7504466	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505283	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506610	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7506974	0.96[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	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093374	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952482	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	esv2566842	chr18:6728880-6730366	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	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
rs7506354	RP11-91I8.3	cis	Muscle Skeletal	GTEx
rs7506354	ARHGAP28	cis	Thyroid	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6721000-6729000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr18:6725200-6729000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr18:6728200-6729000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:6728400-6729000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr18:6728400-6729000	Flanking Active TSS	Fetal Kidney	kidney
6	chr18:6728400-6729000	Flanking Active TSS	Fetal Lung	lung
7	chr18:6728400-6729000	Bivalent Enhancer	NHDF-Ad	bronchial
8	chr18:6728400-6729200	Flanking Active TSS	K562	blood
9	chr18:6728400-6730600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:6728600-6729000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr18:6728600-6729000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr18:6728600-6729000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr18:6728600-6729000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr18:6728600-6729000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr18:6728600-6729000	Flanking Active TSS	Fetal Intestine Large	intestine
16	chr18:6728600-6729000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr18:6728600-6729200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr18:6728600-6729200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr18:6728600-6729200	Flanking Active TSS	HSMM	muscle
20	chr18:6728600-6729200	Flanking Active TSS	NH-A	brain
21	chr18:6728600-6729400	Enhancers	Fetal Heart	heart
22	chr18:6728600-6730600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr18:6728800-6729000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr18:6728800-6729000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr18:6728800-6729000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:6728800-6729000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr18:6728800-6729000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr18:6728800-6729000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:6728800-6729000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:6728800-6729000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr18:6728800-6729000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:6728800-6729000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
33	chr18:6728800-6729000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:6728800-6729000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:6728800-6729000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:6728800-6729000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr18:6728800-6729000	Enhancers	Adipose Nuclei	Adipose
38	chr18:6728800-6729000	Enhancers	Brain Germinal Matrix	brain
39	chr18:6728800-6729000	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr18:6728800-6729000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr18:6728800-6729000	Enhancers	Placenta	Placenta
42	chr18:6728800-6729000	Enhancers	Fetal Stomach	stomach
43	chr18:6728800-6729000	Enhancers	Pancreas	Pancrea
44	chr18:6728800-6729000	Enhancers	Rectal Smooth Muscle	rectum
45	chr18:6728800-6729000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr18:6728800-6729000	Enhancers	Hela-S3	cervix
47	chr18:6728800-6729000	Enhancers	HMEC	breast
48	chr18:6728800-6729200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:6728800-6729200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr18:6728800-6729200	Enhancers	Brain Angular Gyrus	brain

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