Variant report

Variant	rs13196790
Chromosome Location	chr6:128815850-128815851
allele	A/G
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	STAT3	chr6:128815736-128816046	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr6:128815702-128815943	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF7L2	chr6:128815395-128816007	HEK293	kidney:	n/a	n/a
4	FOXA1	chr6:128815439-128815868	HepG2	liver:	n/a	n/a
5	TCF7L2	chr6:128815516-128815980	PANC-1	pancreas:	n/a	n/a
6	FOXA1	chr6:128815379-128815862	HepG2	liver:	n/a	n/a
7	MYC	chr6:128815755-128816096	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF263	chr6:128814892-128816057	HEK293-T-REx	kidney:	n/a	n/a
9	KAP1	chr6:128815551-128816025	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128813517..128817980-chr6:128840263..128842508,4	MCF-7	breast:
2	chr6:128813711..128816701-chr6:128817827..128820787,3	MCF-7	breast:

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10155795	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12717181	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13201242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13216847	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1341597	1.00[CEU][hapmap]
rs1341599	0.91[EUR][1000 genomes]
rs1891150	1.00[CEU][hapmap]
rs28360647	0.97[AFR][1000 genomes]
rs28550449	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705340	0.97[AFR][1000 genomes]
rs34337200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34558551	0.90[AFR][1000 genomes]
rs34760929	0.99[AFR][1000 genomes]
rs34931647	0.97[AFR][1000 genomes]
rs35242805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35395689	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35419289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36120502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58050191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61143917	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6917187	0.80[YRI][hapmap]
rs71568904	0.91[EUR][1000 genomes]
rs71568905	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71568906	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7760626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9482888	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs9482890	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9491951	1.00[CEU][hapmap]
rs9491964	0.91[EUR][1000 genomes]
rs9491967	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9491970	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9491971	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9491972	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9491975	1.00[YRI][hapmap];0.97[AFR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128797400-128822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:128808800-128830800	Weak transcription	Lung	lung
3	chr6:128811800-128816600	Weak transcription	Gastric	stomach
4	chr6:128812000-128817000	Genic enhancers	HepG2	liver
5	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:128812800-128819400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:128813000-128817800	Enhancers	Stomach Mucosa	stomach
8	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:128813200-128819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
11	chr6:128813400-128816800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:128813400-128816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:128813400-128816800	Weak transcription	Left Ventricle	heart
14	chr6:128813400-128817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:128813400-128819200	Weak transcription	Colonic Mucosa	Colon
16	chr6:128813400-128819200	Weak transcription	Fetal Brain Male	brain
17	chr6:128813400-128819400	Weak transcription	Psoas Muscle	Psoas
18	chr6:128813400-128820000	Enhancers	Fetal Intestine Small	intestine
19	chr6:128813400-128820000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:128813600-128816800	Weak transcription	Aorta	Aorta
22	chr6:128813600-128817800	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:128813600-128819200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:128813600-128820400	Weak transcription	HSMM	muscle
25	chr6:128814000-128816600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:128814000-128819200	Weak transcription	NH-A	brain
27	chr6:128814000-128825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:128814200-128816800	Weak transcription	A549	lung
29	chr6:128814200-128818600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:128814200-128819000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:128814200-128819200	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:128814200-128819200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:128814200-128821200	Weak transcription	Osteobl	bone
34	chr6:128814200-128821800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:128814200-128822200	Weak transcription	Fetal Stomach	stomach
36	chr6:128814200-128824800	Weak transcription	Right Ventricle	heart
37	chr6:128814600-128817200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:128814600-128818000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:128814800-128816000	Enhancers	Fetal Lung	lung
40	chr6:128814800-128816400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:128814800-128816800	Enhancers	Small Intestine	intestine
42	chr6:128814800-128817400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:128814800-128817400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:128814800-128817600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:128814800-128819200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr6:128815000-128816400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr6:128815000-128817200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:128815000-128820400	Weak transcription	NHEK	skin
49	chr6:128815000-128821200	Weak transcription	NHLF	lung
50	chr6:128815200-128816000	Active TSS	Brain Cingulate Gyrus	brain

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