Variant report

Variant	rs236452
Chromosome Location	chr6:36702284-36702285
allele	C/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	chr6:36701895-36703832	HL-60	blood:	n/a	n/a
2	POLR2A	chr6:36702134-36704101	NB4	blood:	n/a	n/a
3	POLR2A	chr6:36702248-36702303	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:36701915-36703986	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36692869..36694899-chr6:36700775..36703080,2	MCF-7	breast:
2	chr6:36695657..36698030-chr6:36700581..36702478,2	K562	blood:
3	chr6:36583432..36585248-chr6:36700120..36704013,3	MCF-7	breast:
4	chr6:36561849..36563615-chr6:36700031..36702846,2	K562	blood:

Variant related genes	Relation type
ENSG00000220349	TF binding region
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1010790	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1010791	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1064827	0.87[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs1864750	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236444	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs236465	0.82[ASN][1000 genomes]
rs236482	0.87[CHD][hapmap]
rs236483	0.87[CHD][hapmap]
rs236487	0.87[CHD][hapmap]
rs236489	0.87[CHD][hapmap]
rs236490	0.83[CHD][hapmap]
rs7772191	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9380596	0.82[CEU][hapmap]
rs9394380	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462215	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv885809	chr6:36687518-36719079	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv885810	chr6:36695223-36714491	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv885811	chr6:36695223-36719079	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv885812	chr6:36696904-36705684	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv819609	chr6:36700559-36708943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv520755	chr6:36702284-36713720	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236452	ITPR3	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36689200-36702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:36690400-36702600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:36694000-36703000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:36695800-36702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:36695800-36702800	Weak transcription	Gastric	stomach
6	chr6:36696000-36702600	Weak transcription	NHEK	skin
7	chr6:36697200-36702400	Weak transcription	Adipose Nuclei	Adipose
8	chr6:36697200-36702400	Weak transcription	NHDF-Ad	bronchial
9	chr6:36697400-36702600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:36697600-36702600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:36697600-36702600	Weak transcription	HUVEC	blood vessel
12	chr6:36697800-36702400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:36699200-36703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:36699200-36703400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:36699600-36702400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:36700600-36702400	Weak transcription	Right Atrium	heart
17	chr6:36700800-36702400	Weak transcription	Fetal Brain Male	brain
18	chr6:36701200-36702400	Enhancers	Fetal Muscle Leg	muscle
19	chr6:36701200-36702400	Weak transcription	GM12878-XiMat	blood
20	chr6:36702000-36702800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr6:36702000-36704000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:36702200-36702400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:36702200-36702400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:36702200-36702400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:36702200-36702600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:36702200-36702600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:36702200-36702600	Bivalent Enhancer	Fetal Stomach	stomach
28	chr6:36702200-36702600	Enhancers	NHLF	lung
29	chr6:36702200-36702800	Enhancers	Primary B cells from cord blood	blood
30	chr6:36702200-36702800	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:36702200-36702800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:36702200-36702800	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:36702200-36703800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:36702200-36703800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:36702200-36703800	Enhancers	Spleen	Spleen
36	chr6:36702200-36704000	Enhancers	Esophagus	oesophagus
37	chr6:36702200-36704000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:36702200-36704200	Enhancers	Stomach Mucosa	stomach
39	chr6:36702200-36704800	Enhancers	Lung	lung

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