Variant report

Variant	rs4798487
Chromosome Location	chr18:6731655-6731656
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	CEBPB	chr18:6731286-6731666	IMR90	lung:	n/a	n/a
2	TCF12	chr18:6731016-6731798	SK-N-SH	brain:	n/a	n/a
3	FOS	chr18:6731209-6731683	MCF10A-Er-Src	breast:	n/a	n/a
4	PBX3	chr18:6731097-6731803	SK-N-SH	brain:	n/a	n/a
5	MAX	chr18:6731179-6731675	Hela-S3	cervix:	n/a	chr18:6731481-6731496
6	MYC	chr18:6730632-6731685	MCF10A-Er-Src	breast:	n/a	chr18:6731481-6731496
7	FOS	chr18:6731064-6731945	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr18:6731218-6731717	IMR90	lung:	n/a	n/a
9	MAFK	chr18:6731313-6731896	IMR90	lung:	n/a	chr18:6731836-6731851
10	TCF7L2	chr18:6730454-6731918	HEK293	kidney:	n/a	chr18:6731012-6731022
11	GATA3	chr18:6730991-6731851	SK-N-SH	brain:	n/a	chr18:6731046-6731054 chr18:6731776-6731792
12	TCF12	chr18:6731025-6731863	SK-N-SH	brain:	n/a	n/a
13	MYC	chr18:6731143-6731709	MCF10A-Er-Src	breast:	n/a	chr18:6731481-6731496
14	STAT3	chr18:6731163-6731710	MCF10A-Er-Src	breast:	n/a	chr18:6731380-6731391
15	FOS	chr18:6731073-6731703	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr18:6730859-6731776	MCF10A-Er-Src	breast:	n/a	chr18:6731380-6731391
17	KAP1	chr18:6731315-6731705	HEK293	kidney:	n/a	n/a
18	GATA3	chr18:6731045-6731708	SK-N-SH	brain:	n/a	chr18:6731046-6731054
19	POLR2A	chr18:6731218-6731704	U87	brain:	n/a	n/a
20	EP300	chr18:6731192-6731785	SK-N-SH	brain:	n/a	n/a
21	PBX3	chr18:6731162-6731712	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr18:6731101-6731820	SK-N-SH	brain:	n/a	n/a
23	FOS	chr18:6731143-6731710	MCF10A-Er-Src	breast:	n/a	n/a

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	chr18:6685044..6687268-chr18:6731388..6733678,2	K562	blood:
4	chr18:6715232..6717469-chr18:6730082..6731975,2	K562	blood:
5	chr18:6731530..6734164-chr18:6740298..6742070,2	K562	blood:

Variant related genes	Relation type
ENSG00000266441	TF binding region

Extended variants
information (count: 36 )
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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11660237	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150787	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326891	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12455302	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28463953	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132206	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797256	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55866900	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56061391	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62081458	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505315	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7505419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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: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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4798487	RP11-91I8.3	cis	Muscle Skeletal	GTEx
rs4798487	ARHGAP28	cis	Thyroid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6729000-6731800	Active TSS	Brain Germinal Matrix	brain
2	chr18:6730000-6732000	ZNF genes & repeats	Fetal Brain Male	brain
3	chr18:6730200-6731800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:6730200-6731800	Flanking Active TSS	Osteobl	bone
5	chr18:6730200-6735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:6730200-6747800	Weak transcription	Left Ventricle	heart
7	chr18:6730400-6731800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr18:6730400-6731800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr18:6730400-6731800	Flanking Active TSS	HSMMtube	muscle
10	chr18:6730400-6731800	Flanking Active TSS	HUVEC	blood vessel
11	chr18:6730400-6732000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:6730400-6732200	Enhancers	Hela-S3	cervix
13	chr18:6730400-6735600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr18:6730600-6731800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:6730600-6731800	Enhancers	Colon Smooth Muscle	Colon
16	chr18:6730600-6731800	Enhancers	HMEC	breast
17	chr18:6730600-6732000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:6730800-6731800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr18:6730800-6732000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr18:6730800-6732000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr18:6730800-6733000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr18:6730800-6733000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr18:6730800-6733800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr18:6730800-6734800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:6730800-6738800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr18:6730800-6740400	Weak transcription	Psoas Muscle	Psoas
27	chr18:6730800-6740800	Weak transcription	Right Atrium	heart
28	chr18:6731000-6731800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:6731200-6731800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:6731200-6731800	Enhancers	Fetal Brain Female	brain
31	chr18:6731200-6731800	Flanking Active TSS	NH-A	brain
32	chr18:6731200-6731800	Enhancers	NHEK	skin
33	chr18:6731200-6732000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:6731200-6732000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr18:6731200-6732000	Enhancers	Small Intestine	intestine
36	chr18:6731200-6732200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:6731200-6732200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr18:6731200-6732800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr18:6731200-6732800	Enhancers	Fetal Muscle Leg	muscle
40	chr18:6731200-6733200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr18:6731200-6735600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr18:6731400-6731800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr18:6731400-6731800	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr18:6731400-6731800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr18:6731400-6731800	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr18:6731400-6731800	Flanking Active TSS	Fetal Lung	lung
47	chr18:6731400-6731800	Enhancers	Placenta	Placenta
48	chr18:6731400-6731800	Enhancers	Gastric	stomach
49	chr18:6731400-6731800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr18:6731400-6731800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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