Variant report

Variant	rs2479426
Chromosome Location	chr13:111164198-111164199
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	HMGN3	chr13:111164109-111164510	K562	blood:	n/a	n/a
2	CTCF	chr13:111164060-111164210	HepG2	liver:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
3	CTCF	chr13:111164060-111164210	HCPEpiC	choroid plexus:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
4	MAX	chr13:111163922-111164328	K562	blood:	n/a	chr13:111164098-111164108
5	CTCF	chr13:111163966-111164217	K562	blood:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
6	CCNT2	chr13:111163810-111164238	K562	blood:	n/a	n/a
7	CTCF	chr13:111163910-111164205	K562	blood:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
8	CTCF	chr13:111164060-111164210	BE2_C	brain:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
9	RAD21	chr13:111163973-111164203	HepG2	liver:	n/a	chr13:111164090-111164100 chr13:111164080-111164093
10	E2F6	chr13:111164178-111164339	K562	blood:	n/a	n/a
11	CTCF	chr13:111164060-111164210	HPAF	blood vessel:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
12	MYC	chr13:111163919-111164254	K562	blood:	n/a	chr13:111164098-111164108
13	MAX	chr13:111163956-111164275	NB4	blood:	n/a	chr13:111164098-111164108
14	CTCF	chr13:111164060-111164210	HBMEC	blood vessel:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
15	CTCF	chr13:111163903-111164240	K562	blood:	n/a	chr13:111164232-111164240 chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129 chr13:111164227-111164240
16	RAD21	chr13:111163894-111164216	HepG2	liver:	n/a	chr13:111164090-111164100 chr13:111164080-111164093
17	RAD21	chr13:111163900-111164291	H1-hESC	embryonic stem cell:	n/a	chr13:111164223-111164242 chr13:111164090-111164100 chr13:111164227-111164241 chr13:111164080-111164093
18	CTCF	chr13:111163882-111164222	K562	blood:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129
19	MAX	chr13:111163921-111164224	K562	blood:	n/a	chr13:111164098-111164108
20	MYC	chr13:111163889-111164227	K562	blood:	n/a	chr13:111164098-111164108
21	CTCF	chr13:111164080-111164230	K562	blood:	n/a	chr13:111164087-111164100 chr13:111164081-111164094 chr13:111164116-111164129

No.	Distal block	Cell Line	Cell type
1	chr13:111162545..111165671-chr13:111172658..111175880,3	MCF-7	breast:
2	chr13:111160382..111162246-chr13:111163776..111165316,2	MCF-7	breast:
3	chr13:111156722..111158386-chr13:111162360..111164730,2	MCF-7	breast:
4	chr13:111128717..111130651-chr13:111161918..111164704,2	K562	blood:

Variant related genes	Relation type
COL4A2-AS1	TF binding region
ENSG00000232814	Chromatin interaction
ENSG00000134871	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1049906	0.85[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs15457	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3742186	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422733	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4773202	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6492279	0.85[CEU][hapmap]
rs9515239	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv901009	chr13:111134780-111176393	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv563121	chr13:111155363-111168488	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	n/a
10	nsv984479	chr13:111157297-111176429	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2479426	RAB20	cis	parietal	SCAN
rs2479426	COL4A2	cis	uninvolved skin	skin_eQTL
rs2479426	COL4A2	cis	normal skin	skin_eQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111109800-111168000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr13:111124400-111167400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:111139600-111166400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:111139600-111166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:111140200-111167200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr13:111140800-111166600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:111141600-111165600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:111143400-111166800	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr13:111150000-111165000	Weak transcription	Brain Angular Gyrus	brain
10	chr13:111150800-111167200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:111152600-111168000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:111152800-111165800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:111153000-111168000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:111153400-111172800	Weak transcription	Brain Substantia Nigra	brain
15	chr13:111155200-111175600	Weak transcription	Fetal Thymus	thymus
16	chr13:111159600-111166600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:111159600-111166800	Strong transcription	HUVEC	blood vessel
18	chr13:111159600-111167600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:111159600-111172200	Weak transcription	Brain Hippocampus Middle	brain
20	chr13:111159600-111176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:111159800-111167800	Strong transcription	NH-A	brain
22	chr13:111159800-111167800	Strong transcription	Osteobl	bone
23	chr13:111159800-111168200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:111160000-111165600	Strong transcription	NHEK	skin
25	chr13:111160000-111167000	Strong transcription	HSMM	muscle
26	chr13:111160000-111167800	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr13:111160000-111172800	Weak transcription	Brain Anterior Caudate	brain
28	chr13:111160200-111165600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:111160200-111167600	Strong transcription	Aorta	Aorta
30	chr13:111160600-111165600	Strong transcription	Colon Smooth Muscle	Colon
31	chr13:111160800-111167800	Strong transcription	Lung	lung
32	chr13:111160800-111172200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:111160800-111172600	Weak transcription	Esophagus	oesophagus
34	chr13:111160800-111176400	Weak transcription	Psoas Muscle	Psoas
35	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr13:111161000-111164200	Weak transcription	Liver	Liver
37	chr13:111161000-111168000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:111161200-111173000	Weak transcription	Brain Germinal Matrix	brain
39	chr13:111161400-111164200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr13:111161600-111165200	Strong transcription	Fetal Brain Female	brain
41	chr13:111162000-111164400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr13:111162000-111165000	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr13:111162000-111167400	Strong transcription	Ovary	ovary
44	chr13:111162400-111165600	Strong transcription	NHLF	lung
45	chr13:111162400-111173000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:111162600-111164200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr13:111162600-111164800	Weak transcription	HMEC	breast
48	chr13:111162600-111166400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:111162600-111166400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr13:111162600-111168000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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