Variant report

Variant	rs11123024
Chromosome Location	chr2:112653802-112653803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr2:112653618-112653866	K562	blood:	n/a	n/a
2	RCOR1	chr2:112653616-112654100	K562	blood:	n/a	n/a
3	HCFC1	chr2:112653748-112654222	K562	blood:	n/a	n/a
4	MYC	chr2:112653622-112653960	K562	blood:	n/a	n/a
5	UBTF	chr2:112653732-112653809	K562	blood:	n/a	n/a
6	TBL1XR1	chr2:112653493-112654033	K562	blood:	n/a	n/a
7	JUND	chr2:112653524-112653881	K562	blood:	n/a	n/a
8	CEBPB	chr2:112653264-112654209	K562	blood:	n/a	chr2:112653372-112653381 chr2:112653394-112653405 chr2:112653370-112653381
9	TBP	chr2:112653537-112653875	K562	blood:	n/a	n/a
10	FOXA2	chr2:112653625-112653872	HepG2	liver:	n/a	n/a
11	IRF1	chr2:112653468-112653898	K562	blood:	n/a	n/a
12	TAL1	chr2:112653769-112654125	K562	blood:	n/a	n/a
13	POLR2A	chr2:112653678-112653838	K562	blood:	n/a	n/a
14	POLR2A	chr2:112653789-112653904	MCF10A-Er-Src	breast:	n/a	n/a
15	ZNF263	chr2:112653486-112654687	HEK293-T-REx	kidney:	n/a	n/a
16	MAX	chr2:112653583-112653868	K562	blood:	n/a	n/a
17	MAZ	chr2:112653314-112654026	K562	blood:	n/a	n/a
18	TEAD4	chr2:112653544-112654072	K562	blood:	n/a	n/a
19	UBTF	chr2:112653583-112653806	K562	blood:	n/a	n/a
20	TBP	chr2:112653637-112653971	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr2:112653590-112653916	K562	blood:	n/a	n/a
22	RCOR1	chr2:112653571-112654217	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:112641916..112643475-chr2:112652986..112654770,2	MCF-7	breast:
2	chr2:112640266..112649080-chr2:112649576..112660203,14	MCF-7	breast:
3	chr2:112652127..112657107-chr2:112810449..112814378,4	K562	blood:
4	chr2:112651539..112654934-chr2:112657187..112660968,3	K562	blood:
5	chr2:112645445..112647552-chr2:112653399..112655152,2	K562	blood:

No data

Variant related genes	Relation type
MERTK	TF binding region
ENSG00000236307	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000153107	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10175316	0.81[ASN][1000 genomes]
rs11123035	0.82[ASN][1000 genomes]
rs12992449	0.82[ASN][1000 genomes]
rs13391947	0.82[ASN][1000 genomes]
rs13397063	0.82[ASN][1000 genomes]
rs1400322	0.82[ASN][1000 genomes]
rs1400323	0.82[ASN][1000 genomes]
rs1516639	0.82[ASN][1000 genomes]
rs1516640	0.82[ASN][1000 genomes]
rs1607060	0.82[ASN][1000 genomes]
rs2311813	0.82[ASN][1000 genomes]
rs4290663	0.82[ASN][1000 genomes]
rs4848908	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55757240	0.81[ASN][1000 genomes]
rs56097129	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56822761	0.96[ASN][1000 genomes]
rs59219838	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62162478	0.86[EUR][1000 genomes]
rs7569614	0.81[ASN][1000 genomes]
rs7571447	0.82[ASN][1000 genomes]
rs869016	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
5	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv834333	chr2:112490211-112658347	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
9	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
10	nsv961869	chr2:112645626-112660962	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv998028	chr2:112649472-112734015	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv582701	chr2:112649472-112740597	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv526647	chr2:112651316-112738562	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv582702	chr2:112651316-112738562	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11123024	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112642600-112654400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:112642600-112655000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:112642600-112655000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:112642600-112655000	Weak transcription	Right Atrium	heart
5	chr2:112642800-112655000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:112646200-112655000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:112651600-112655000	Weak transcription	Liver	Liver
8	chr2:112653200-112654000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:112653200-112655000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:112653200-112655000	Enhancers	K562	blood
11	chr2:112653400-112655000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:112653600-112654000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:112653600-112654000	Enhancers	Stomach Mucosa	stomach
14	chr2:112653600-112654800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:112653600-112654800	Enhancers	HepG2	liver
16	chr2:112653600-112655000	Enhancers	Fetal Heart	heart
17	chr2:112653600-112655200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:112653600-112655400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:112653600-112655400	Enhancers	Esophagus	oesophagus
20	chr2:112653600-112655400	Enhancers	Spleen	Spleen
21	chr2:112653800-112654000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:112653800-112654000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:112653800-112654000	Enhancers	Lung	lung
24	chr2:112653800-112654200	Enhancers	Fetal Thymus	thymus
25	chr2:112653800-112654600	Enhancers	HMEC	breast
26	chr2:112653800-112654600	Enhancers	NHEK	skin
27	chr2:112653800-112654800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:112653800-112655000	Weak transcription	Colonic Mucosa	Colon
29	chr2:112653800-112655200	Enhancers	Placenta	Placenta

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