Variant report

Variant	rs61103246
Chromosome Location	chr13:111262934-111262935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr13:111262275-111263255	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr13:111262211-111263261	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr13:111262237-111263180	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr13:111262318-111263162	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr13:111262253-111263160	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr13:111262221-111263366	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr13:111262371-111263152	ECC-1	luminal epithelium:	n/a	n/a
8	SIN3A	chr13:111262837-111263037	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD2	chr13:111262924-111262934	H1-hESC	embryonic stem cell:	n/a	n/a
10	NFIC	chr13:111262213-111263276	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr13:111262242-111263235	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr13:111262166-111263143	ECC-1	luminal epithelium:	n/a	n/a
13	EBF1	chr13:111262714-111263049	GM12878	blood:	n/a	chr13:111262889-111262900

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111260500..111264112-chr13:111364498..111367166,4	K562	blood:
2	chr13:111260059..111265177-chr13:111265738..111269909,6	K562	blood:
3	chr13:111262796..111264408-chr13:111266461..111269067,2	K562	blood:
4	chr13:111262131..111264525-chr13:111366020..111367721,2	MCF-7	breast:

No data

Variant related genes	Relation type
CARKD	TF binding region
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041143	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1041173	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11069855	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11069856	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11620520	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12428965	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12429905	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12430333	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12583083	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2011692	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2148081	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274411	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28384426	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742193	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742194	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742196	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3783097	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825465	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825466	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825467	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3956684	0.83[ASN][1000 genomes]
rs4771700	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4771701	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4773230	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661645	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661647	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661650	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661656	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661657	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7322067	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7323602	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7981194	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7981780	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7991671	0.87[ASN][1000 genomes]
rs7995119	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9555721	0.84[ASN][1000 genomes]
rs9583513	0.90[ASN][1000 genomes]
rs9583514	0.90[ASN][1000 genomes]
rs9583518	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9588207	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9588209	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9588214	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats 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 target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats 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
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS 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
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1038089	chr13:111229517-111274823	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
15	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61103246	AL139385.1	cis	Muscle Skeletal	GTEx
rs61103246	CARKD	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111260800-111264000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:111262000-111263200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:111262000-111263200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr13:111262000-111263400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:111262000-111263400	Enhancers	NHEK	skin
6	chr13:111262000-111264200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr13:111262200-111263200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:111262400-111263200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:111262400-111263400	Flanking Active TSS	GM12878-XiMat	blood
10	chr13:111262600-111263000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr13:111262600-111263000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:111262600-111263000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr13:111262600-111263000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr13:111262600-111263000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr13:111262600-111263000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr13:111262600-111263000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:111262600-111263000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:111262600-111263000	Enhancers	Brain Anterior Caudate	brain
19	chr13:111262600-111263000	Enhancers	Esophagus	oesophagus
20	chr13:111262600-111263000	Enhancers	Fetal Kidney	kidney
21	chr13:111262600-111263000	Enhancers	HMEC	breast
22	chr13:111262600-111263200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:111262600-111263400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:111262600-111263400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:111262600-111263400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:111262600-111263400	Enhancers	Placenta	Placenta
27	chr13:111262600-111263400	Enhancers	HepG2	liver
28	chr13:111262600-111265200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr13:111262600-111267200	Weak transcription	HSMM	muscle
30	chr13:111262800-111263200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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