Variant report

Variant	rs57888387
Chromosome Location	chr7:150004244-150004245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr7:150004174-150004670	K562	blood:	n/a	n/a
2	GATA2	chr7:150004223-150004652	K562	blood:	n/a	n/a
3	NR2F2	chr7:150004173-150004649	K562	blood:	n/a	n/a
4	KAP1	chr7:150004021-150004810	K562	blood:	n/a	n/a
5	CBX3	chr7:150004239-150004629	K562	blood:	n/a	n/a
6	CBX3	chr7:150004208-150004572	HCT-116	colon:	n/a	n/a
7	NR2F2	chr7:150004087-150004711	K562	blood:	n/a	n/a
8	CBX3	chr7:150004138-150004672	K562	blood:	n/a	n/a
9	SETDB1	chr7:150003971-150004529	U2OS	brain:	n/a	n/a
10	ARID3A	chr7:150004069-150004434	K562	blood:	n/a	n/a
11	ATF1	chr7:150004234-150004547	K562	blood:	n/a	n/a
12	TRIM28	chr7:150004123-150004662	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150002516..150004738-chr7:150017976..150020518,2	K562	blood:
2	chr7:150003788..150006557-chr7:150126189..150128283,2	K562	blood:
3	chr7:150002193..150004738-chr7:150017976..150020637,3	K562	blood:

No data

Variant related genes	Relation type
ACTR3C	TF binding region
ENSG00000127399	Chromatin interaction
ENSG00000106526	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1047207	0.84[EUR][1000 genomes]
rs1047575	0.81[EUR][1000 genomes]
rs1047586	0.81[EUR][1000 genomes]
rs10952249	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10952250	0.84[EUR][1000 genomes]
rs1132261	0.87[AFR][1000 genomes]
rs11764936	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11765644	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11765692	0.85[EUR][1000 genomes]
rs11766288	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11767726	0.88[EUR][1000 genomes]
rs11769348	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11773351	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11974980	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11975886	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11983355	0.88[EUR][1000 genomes]
rs13223702	0.87[AFR][1000 genomes]
rs1464752	0.82[EUR][1000 genomes]
rs1464753	0.85[EUR][1000 genomes]
rs17173617	0.84[EUR][1000 genomes]
rs17837498	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1916932	0.85[EUR][1000 genomes]
rs1962004	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1983440	0.85[EUR][1000 genomes]
rs2098053	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2108851	0.88[EUR][1000 genomes]
rs2108852	0.88[EUR][1000 genomes]
rs2108853	0.88[EUR][1000 genomes]
rs2108854	0.88[EUR][1000 genomes]
rs2159234	0.88[EUR][1000 genomes]
rs2159235	0.88[EUR][1000 genomes]
rs2159236	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2373751	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088207	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34489187	0.94[AFR][1000 genomes]
rs34728606	0.87[AFR][1000 genomes]
rs36069544	0.81[AFR][1000 genomes]
rs3735167	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3735169	0.90[EUR][1000 genomes]
rs3735170	0.90[EUR][1000 genomes]
rs3735171	0.91[EUR][1000 genomes]
rs3735172	0.85[EUR][1000 genomes]
rs3735173	0.87[EUR][1000 genomes]
rs3735174	0.87[EUR][1000 genomes]
rs3735175	0.88[EUR][1000 genomes]
rs3800780	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3800781	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4395803	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4554381	0.84[EUR][1000 genomes]
rs55715989	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55881542	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55974958	0.84[EUR][1000 genomes]
rs56019796	0.92[EUR][1000 genomes]
rs56190213	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56402329	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56923535	0.92[EUR][1000 genomes]
rs56998970	0.93[EUR][1000 genomes]
rs59572505	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60268791	0.83[EUR][1000 genomes]
rs60283368	0.85[EUR][1000 genomes]
rs60467296	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61421252	0.84[EUR][1000 genomes]
rs6964110	0.83[EUR][1000 genomes]
rs73170169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170174	0.88[EUR][1000 genomes]
rs73170185	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170192	0.80[EUR][1000 genomes]
rs7781827	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7788316	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7806429	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs883138	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889435	chr7:149585379-150013393	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription 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	75 gene(s)	inside rSNPs	diseases
3	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv981608	chr7:150002640-150009746	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs57888387	ACTR3C	cis	Muscle Skeletal	GTEx
rs57888387	LRRC61	cis	Nerve Tibial	GTEx
rs57888387	LRRC61	cis	Esophagus Mucosa	GTEx
rs57888387	RARRES2	cis	multi-tissue	Pritchard
rs57888387	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs57888387	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs57888387	LRRC61	cis	Thyroid	GTEx
rs57888387	LRRC61	cis	Muscle Skeletal	GTEx
rs57888387	LRRC61	cis	lung	GTEx
rs57888387	LRRC61	cis	Artery Tibial	GTEx
rs57888387	REPIN1	cis	Muscle Skeletal	GTEx
rs57888387	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs57888387	LRRC61	cis	Adipose Subcutaneous	GTEx
rs57888387	LRRC61	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149984200-150012400	Weak transcription	Liver	Liver
2	chr7:149984200-150019400	Weak transcription	Colonic Mucosa	Colon
3	chr7:149992400-150018000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:150000400-150006600	Enhancers	K562	blood
5	chr7:150001800-150005000	Enhancers	Hela-S3	cervix
6	chr7:150002600-150004600	Weak transcription	HepG2	liver
7	chr7:150002600-150007200	Weak transcription	Pancreas	Pancrea
8	chr7:150003600-150004400	Enhancers	Fetal Thymus	thymus
9	chr7:150003800-150016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:150004000-150019000	Weak transcription	Primary hematopoietic stem cells	blood

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