Variant report

Variant	rs12429905
Chromosome Location	chr13:111266865-111266866
allele	A/C/G/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	POLR2A	chr13:111266863-111266942	HepG2	liver:	n/a	n/a
2	MAFK	chr13:111266785-111266974	HepG2	liver:	n/a	chr13:111266889-111266904
3	MAFK	chr13:111266833-111267025	HepG2	liver:	n/a	chr13:111266889-111266904
4	STAT3	chr13:111266743-111266871	MCF10A-Er-Src	breast:	n/a	chr13:111266748-111266759
5	STAT3	chr13:111266726-111266897	MCF10A-Er-Src	breast:	n/a	chr13:111266748-111266759
6	POLR2A	chr13:111266809-111269041	GM12878	blood:	n/a	n/a
7	MAFF	chr13:111266795-111266957	HepG2	liver:	n/a	n/a
8	MAFF	chr13:111266830-111266904	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:111266678..111269187-chr13:111295319..111298212,3	MCF-7	breast:
2	chr13:111266655..111268705-chr13:111294879..111298471,3	K562	blood:
3	chr13:111266587..111269692-chr13:111357018..111359356,4	K562	blood:
4	chr13:111265515..111270086-chr13:111364987..111368051,5	MCF-7	breast:
5	chr13:111266746..111269387-chr13:111357064..111359748,3	MCF-7	breast:
6	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:
7	chr13:111266737..111268751-chr13:111366724..111368921,2	K562	blood:

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

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1041143	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1041173	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11069855	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11069856	0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11620520	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12428965	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12430333	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12583083	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1853861	0.80[JPT][hapmap]
rs2011692	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2148081	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274411	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28384426	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742193	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3742194	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3742196	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3783097	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825465	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825466	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825467	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4771700	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4771701	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4771702	0.80[JPT][hapmap]
rs4771703	0.80[JPT][hapmap]
rs4771704	0.80[JPT][hapmap]
rs4773230	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773232	0.80[JPT][hapmap]
rs61103246	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72661645	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72661647	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72661650	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72661656	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72661657	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7322067	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7323602	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7981194	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7981780	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7991671	0.84[ASN][1000 genomes]
rs7995119	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998859	1.00[YRI][hapmap]
rs9583513	0.82[ASN][1000 genomes]
rs9583514	0.82[ASN][1000 genomes]
rs9583518	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9583520	0.80[JPT][hapmap]
rs9588207	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9588209	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9588214	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
18	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12429905	TNFSF13B	cis	cerebellum	SCAN
rs12429905	CARKD	cis	Muscle Skeletal	GTEx
rs12429905	CARKD	cis	cerebellum	SCAN
rs12429905	TUBGCP3	cis	parietal	SCAN
rs12429905	AL139385.1	cis	Muscle Skeletal	GTEx
rs12429905	CARKD	cis	parietal	SCAN
rs12429905	GRTP1	cis	cerebellum	SCAN
rs12429905	PCID2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111262600-111267200	Weak transcription	HSMM	muscle
2	chr13:111263000-111267000	Weak transcription	Esophagus	oesophagus
3	chr13:111263000-111267200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:111263000-111267200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:111263000-111267400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:111263000-111267400	Weak transcription	Fetal Kidney	kidney
7	chr13:111263200-111267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:111263200-111267400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:111263400-111267200	Weak transcription	Placenta	Placenta
10	chr13:111263400-111267400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:111263600-111267400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr13:111263800-111267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:111264000-111267000	Weak transcription	Hela-S3	cervix
14	chr13:111264000-111267200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:111264000-111267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr13:111264000-111267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:111264000-111267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:111264000-111267400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:111264200-111267200	Weak transcription	NHEK	skin
20	chr13:111264200-111267400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr13:111264200-111267400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:111264200-111267400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr13:111264400-111267000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:111264400-111267200	Weak transcription	Brain Anterior Caudate	brain
25	chr13:111264400-111267200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr13:111264400-111267400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:111264600-111267000	Weak transcription	GM12878-XiMat	blood
28	chr13:111265200-111267800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:111265800-111267000	Weak transcription	HepG2	liver
30	chr13:111266400-111267200	Weak transcription	Ovary	ovary
31	chr13:111266800-111267000	Enhancers	Dnd41	blood
32	chr13:111266800-111267200	Active TSS	Stomach Smooth Muscle	stomach
33	chr13:111266800-111267400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle

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