Variant report

Variant	rs13219894
Chromosome Location	chr6:36854104-36854105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:32888988..32889628-chr6:36853240..36854214,2	Hela-S3	cervix:
2	chr6:36841771..36843991-chr6:36852556..36855136,3	MCF-7	breast:
3	chr6:36563465..36565521-chr6:36853930..36855526,2	K562	blood:
4	chr6:36853681..36855481-chr6:36934818..36937310,2	K562	blood:
5	chr6:36852278..36855515-chr6:36952430..36957026,4	MCF-7	breast:
6	chr6:36803997..36809047-chr6:36852852..36856509,4	K562	blood:
7	chr6:36852138..36856054-chr6:36953606..36956862,5	K562	blood:
8	chr6:36853647..36856578-chr6:36948651..36952350,3	K562	blood:
9	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:
10	chr6:36853734..36855339-chr6:37016724..37019565,3	K562	blood:
11	chr6:36560243..36562699-chr6:36853442..36856379,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000189167	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000139618	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1008027	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10456446	0.82[ASN][1000 genomes]
rs10498736	0.81[ASN][1000 genomes]
rs10947638	0.88[ASN][1000 genomes]
rs10947639	0.88[ASN][1000 genomes]
rs10947645	0.83[CHB][hapmap]
rs10947649	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs11757380	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs11759158	0.80[CEU][hapmap]
rs11963298	0.83[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11970506	0.85[ASN][1000 genomes]
rs12194154	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs12202755	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs12213912	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12660916	0.80[CEU][hapmap]
rs12660989	0.80[CEU][hapmap]
rs13190998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192293	0.80[CEU][hapmap]
rs13205292	0.80[CEU][hapmap]
rs13207209	0.80[CEU][hapmap]
rs13219913	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13220210	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16889252	0.82[ASN][1000 genomes]
rs17552005	0.80[CEU][hapmap]
rs2293391	0.86[ASN][1000 genomes]
rs2293392	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs34031451	0.94[ASN][1000 genomes]
rs34605868	0.81[ASN][1000 genomes]
rs34651740	0.93[ASN][1000 genomes]
rs35168332	0.96[ASN][1000 genomes]
rs35423793	0.96[ASN][1000 genomes]
rs3798469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3957238	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4714023	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs61006307	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457961	0.84[ASN][1000 genomes]
rs67540019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901884	0.83[CHB][hapmap]
rs6930737	0.92[ASN][1000 genomes]
rs729659	0.91[ASN][1000 genomes]
rs73418121	0.84[ASN][1000 genomes]
rs73418143	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757241	0.81[ASN][1000 genomes]
rs9296200	0.81[JPT][hapmap]
rs9462232	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9462233	0.90[ASN][1000 genomes]
rs9462234	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs9462235	0.95[ASN][1000 genomes]
rs9462236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470422	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9470425	0.80[CEU][hapmap]
rs9470429	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470440	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9918461	0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs997674	1.00[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13219894	ZNF76	cis	cerebellum	SCAN
rs13219894	C6orf89	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36853000-36855000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:36853200-36854200	Active TSS	Left Ventricle	heart
3	chr6:36853200-36854200	Active TSS	Pancreas	Pancrea
4	chr6:36853200-36854400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:36853200-36854400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:36853200-36854400	Active TSS	Brain Germinal Matrix	brain
7	chr6:36853200-36854400	Active TSS	Colonic Mucosa	Colon
8	chr6:36853200-36854400	Active TSS	Ovary	ovary
9	chr6:36853200-36854600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:36853200-36854600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:36853200-36854600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:36853200-36854600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:36853200-36854600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr6:36853200-36854600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:36853200-36854600	Active TSS	Fetal Brain Male	brain
16	chr6:36853200-36854600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:36853200-36854600	Active TSS	Right Atrium	heart
18	chr6:36853200-36854600	Active TSS	Right Ventricle	heart
19	chr6:36853200-36854600	Active TSS	A549	lung
20	chr6:36853200-36854600	Active TSS	HSMMtube	muscle
21	chr6:36853200-36854800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:36853200-36854800	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:36853200-36854800	Active TSS	Fetal Muscle Trunk	muscle
24	chr6:36853200-36854800	Active TSS	Psoas Muscle	Psoas
25	chr6:36853200-36855000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:36853400-36854200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:36853400-36854200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:36853400-36854200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:36853400-36854200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:36853400-36854200	Active TSS	Aorta	Aorta
31	chr6:36853400-36854200	Active TSS	Brain Substantia Nigra	brain
32	chr6:36853400-36854200	Active TSS	Fetal Intestine Large	intestine
33	chr6:36853400-36854200	Active TSS	Gastric	stomach
34	chr6:36853400-36854200	Active TSS	Lung	lung
35	chr6:36853400-36854200	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr6:36853400-36854400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:36853400-36854400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:36853400-36854400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36853400-36854400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:36853400-36854400	Active TSS	Fetal Brain Female	brain
41	chr6:36853400-36854400	Active TSS	Fetal Heart	heart
42	chr6:36853400-36854400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:36853400-36854400	Bivalent/Poised TSS	HepG2	liver
44	chr6:36853400-36854600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:36853400-36854600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:36853400-36854600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:36853400-36854600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:36853400-36854600	Active TSS	Brain Anterior Caudate	brain
49	chr6:36853400-36854600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr6:36853400-36854800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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