Variant report

Variant	rs13220210
Chromosome Location	chr6:36831525-36831526
allele	G/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36830142..36832721-chr6:36892785..36895215,2	K562	blood:
2	chr6:36817709..36820546-chr6:36830678..36833403,3	MCF-7	breast:
3	chr6:36584813..36586612-chr6:36830505..36832911,2	K562	blood:
4	chr6:36649332..36651548-chr6:36829968..36831540,2	MCF-7	breast:
5	chr6:36749029..36752383-chr6:36830307..36832298,3	MCF-7	breast:
6	chr6:36828665..36833827-chr6:36838293..36844932,14	MCF-7	breast:
7	chr6:36821600..36824429-chr6:36828707..36831696,2	MCF-7	breast:
8	chr6:36561665..36563216-chr6:36830142..36832208,2	MCF-7	breast:
9	chr6:36719279..36721596-chr6:36829791..36832062,2	MCF-7	breast:
10	chr6:36799434..36803274-chr6:36828928..36832166,3	MCF-7	breast:
11	chr6:36752311..36754452-chr6:36830186..36832199,2	K562	blood:
12	chr6:36645491..36648229-chr6:36828778..36831723,2	MCF-7	breast:
13	chr6:36827534..36831660-chr6:36847624..36850020,3	K562	blood:
14	chr6:36829835..36831683-chr6:36855504..36857194,2	K562	blood:
15	chr6:36824608..36827747-chr6:36828662..36831930,3	MCF-7	breast:
16	chr6:36829409..36831916-chr6:36832480..36835667,3	MCF-7	breast:
17	chr6:36562362..36564787-chr6:36830127..36831778,2	K562	blood:
18	chr6:36830465..36834114-chr6:36840024..36843322,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1008027	0.85[ASN][1000 genomes]
rs10456446	0.80[ASN][1000 genomes]
rs10947638	0.86[ASN][1000 genomes]
rs10947639	0.86[ASN][1000 genomes]
rs10947649	0.85[ASN][1000 genomes]
rs11757380	0.81[ASN][1000 genomes]
rs11963298	0.85[ASN][1000 genomes]
rs11970506	0.84[ASN][1000 genomes]
rs12194154	0.88[ASN][1000 genomes]
rs12202755	0.81[ASN][1000 genomes]
rs12213912	0.88[ASN][1000 genomes]
rs13190998	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219894	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219913	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889252	0.80[ASN][1000 genomes]
rs2293391	0.85[ASN][1000 genomes]
rs2293392	0.81[ASN][1000 genomes]
rs34031451	0.96[ASN][1000 genomes]
rs34651740	0.95[ASN][1000 genomes]
rs35168332	0.97[ASN][1000 genomes]
rs35423793	0.97[ASN][1000 genomes]
rs3798469	0.98[ASN][1000 genomes]
rs3957238	0.80[ASN][1000 genomes]
rs4714023	0.80[ASN][1000 genomes]
rs61006307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457961	0.86[ASN][1000 genomes]
rs67540019	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930737	0.94[ASN][1000 genomes]
rs729659	0.92[ASN][1000 genomes]
rs73418121	0.85[ASN][1000 genomes]
rs73418143	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462232	0.96[ASN][1000 genomes]
rs9462233	0.89[ASN][1000 genomes]
rs9462234	0.96[ASN][1000 genomes]
rs9462235	0.93[ASN][1000 genomes]
rs9462236	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470422	0.97[ASN][1000 genomes]
rs9470429	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918461	0.85[ASN][1000 genomes]
rs997674	0.82[ASN][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	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	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13220210	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
2	chr6:36817200-36833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
4	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
5	chr6:36819000-36840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:36819400-36834000	Strong transcription	Dnd41	blood
7	chr6:36819400-36841800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:36819600-36833400	Strong transcription	Primary T cells from cord blood	blood
9	chr6:36819800-36839800	Strong transcription	Fetal Thymus	thymus
10	chr6:36821000-36841400	Weak transcription	Small Intestine	intestine
11	chr6:36821800-36839800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:36821800-36841400	Weak transcription	HSMMtube	muscle
13	chr6:36823600-36832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:36823600-36841400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:36823800-36831600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:36823800-36833600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:36824200-36833800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:36824400-36832400	Weak transcription	HSMM	muscle
19	chr6:36824400-36836600	Weak transcription	Adipose Nuclei	Adipose
20	chr6:36824600-36831600	Weak transcription	Esophagus	oesophagus
21	chr6:36824600-36834000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:36824600-36838600	Weak transcription	Psoas Muscle	Psoas
23	chr6:36825000-36834000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:36826200-36839800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:36826400-36833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:36826400-36841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:36826800-36840000	Strong transcription	Fetal Stomach	stomach
28	chr6:36826800-36841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:36827000-36834600	Weak transcription	Ovary	ovary
30	chr6:36827000-36841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:36827000-36841400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:36827000-36841400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:36827400-36834600	Strong transcription	Fetal Muscle Leg	muscle
34	chr6:36827600-36839400	Strong transcription	HepG2	liver
35	chr6:36827600-36840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:36827800-36840600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:36828000-36832800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:36828000-36833000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:36828000-36838200	Strong transcription	Hela-S3	cervix
40	chr6:36828000-36838800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr6:36828000-36841400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:36828200-36831800	Weak transcription	Right Ventricle	heart
43	chr6:36828200-36839800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr6:36828200-36841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:36828600-36833200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:36828600-36836600	Strong transcription	Primary B cells from cord blood	blood
47	chr6:36828600-36841000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:36828800-36841200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:36829000-36836000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr6:36829000-36840400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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