Variant report

Variant	rs13204228
Chromosome Location	chr6:30734255-30734256
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	TFAP2C	chr6:30734229-30734692	Hela-S3	cervix:	n/a	n/a
2	JUN	chr6:30734134-30739038	K562	blood:	n/a	chr6:30737512-30737521 chr6:30737576-30737586 chr6:30737576-30737586 chr6:30737576-30737586 chr6:30737513-30737520 chr6:30737576-30737586 chr6:30737511-30737520 chr6:30737511-30737521

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30708700..30710764-chr6:30734085..30735975,2	K562	blood:

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11751327	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13213330	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131035	0.92[ASN][1000 genomes]
rs34306534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34682678	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35391600	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35597154	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711231	0.90[AMR][1000 genomes]
rs9800523	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13204228	CCHCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30720600-30736600	Weak transcription	Gastric	stomach
2	chr6:30726800-30739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30728000-30737000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30728200-30736400	Weak transcription	Lung	lung
5	chr6:30728200-30736600	Weak transcription	Aorta	Aorta
6	chr6:30731000-30734600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30731000-30735600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:30731000-30738800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:30731200-30734600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:30731600-30735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:30732000-30735200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:30732000-30735400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:30732000-30735400	Weak transcription	Thymus	Thymus
14	chr6:30732000-30736200	Weak transcription	Esophagus	oesophagus
15	chr6:30732000-30736400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:30732000-30736400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:30732000-30736600	Weak transcription	HSMM	muscle
18	chr6:30732000-30736800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:30732200-30734400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:30732200-30734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:30732200-30734800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:30732200-30735400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:30732200-30735600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:30732200-30736200	Weak transcription	NHLF	lung
25	chr6:30732200-30736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30732200-30736400	Weak transcription	NHDF-Ad	bronchial
27	chr6:30732200-30736600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:30732200-30736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:30732200-30737000	Weak transcription	Fetal Lung	lung
30	chr6:30732400-30734400	Weak transcription	Primary T cells from cord blood	blood
31	chr6:30732400-30734400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:30732400-30734400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:30732400-30734400	Weak transcription	Fetal Thymus	thymus
34	chr6:30732400-30735000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:30732400-30735400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:30732400-30735400	Weak transcription	Dnd41	blood
37	chr6:30732400-30735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:30732400-30735800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:30732400-30736000	Weak transcription	HMEC	breast
40	chr6:30732400-30736200	Weak transcription	Fetal Stomach	stomach
41	chr6:30732400-30736400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:30732400-30736400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:30732400-30736400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:30732400-30736400	Enhancers	A549	lung
45	chr6:30732400-30736400	Enhancers	HepG2	liver
46	chr6:30732400-30736400	Weak transcription	HSMMtube	muscle
47	chr6:30732400-30736600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:30732400-30736600	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:30732400-30736600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:30732400-30736800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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