Variant report

Variant	rs542441
Chromosome Location	chr6:33675851-33675852
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33673686..33677249-chr6:33690275..33693823,3	K562	blood:
2	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
3	chr6:33674390..33676592-chr6:34040123..34042729,2	MCF-7	breast:
4	chr6:33673158..33676456-chr6:33698317..33701048,3	MCF-7	breast:
5	chr6:33674734..33677061-chr6:34117510..34119427,2	K562	blood:
6	chr6:33545816..33547496-chr6:33675270..33677360,2	K562	blood:
7	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
8	chr6:33674250..33675922-chr6:33684521..33687700,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266509	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000197251	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10947435	0.81[JPT][hapmap]
rs11759396	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2229642	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2281829	0.85[CHD][hapmap]
rs2296736	0.88[ASN][1000 genomes]
rs2296741	0.87[ASN][1000 genomes]
rs2296742	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2966	0.85[CHD][hapmap]
rs3818523	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3818525	0.90[ASN][1000 genomes]
rs3818527	0.85[CHD][hapmap]
rs3818529	0.90[ASN][1000 genomes]
rs4711336	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4711337	0.90[ASN][1000 genomes]
rs4711338	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4711343	0.81[JPT][hapmap]
rs4713658	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs4713670	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4713671	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs4713672	0.81[JPT][hapmap]
rs4713674	0.81[JPT][hapmap]
rs4713675	0.81[JPT][hapmap]
rs560111	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs622917	0.92[CHD][hapmap];0.81[JPT][hapmap]
rs626156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6919321	0.81[JPT][hapmap]
rs754404	0.90[ASN][1000 genomes]
rs764752	0.88[ASN][1000 genomes]
rs764754	0.88[ASN][1000 genomes]
rs7759668	0.85[CHD][hapmap]
rs791902	0.90[JPT][hapmap]
rs791903	0.90[JPT][hapmap]
rs9348924	0.86[JPT][hapmap]
rs9394163	0.85[CHD][hapmap]
rs942641	0.81[JPT][hapmap]
rs942643	0.85[CHD][hapmap]
rs9469583	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs542441	ITPR3	cis	Whole Blood	GTEx
rs542441	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
2	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
3	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
7	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
8	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
9	chr6:33665600-33678200	Weak transcription	NH-A	brain
10	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:33665800-33676600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:33666000-33676200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:33666000-33676600	Weak transcription	Brain Angular Gyrus	brain
14	chr6:33666000-33677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:33666000-33678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:33666200-33677600	Weak transcription	Psoas Muscle	Psoas
17	chr6:33666400-33677800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:33666600-33677800	Weak transcription	Right Atrium	heart
19	chr6:33666600-33678200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:33666600-33678400	Weak transcription	Colonic Mucosa	Colon
21	chr6:33666600-33678400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:33667000-33678400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:33667200-33676000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:33667200-33676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:33668400-33677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:33668600-33676000	Weak transcription	Pancreas	Pancrea
27	chr6:33668600-33676000	Weak transcription	Right Ventricle	heart
28	chr6:33668600-33676200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:33668600-33676200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:33668600-33677800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:33668600-33677800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:33668600-33678000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:33668600-33678200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:33668600-33678200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:33668800-33676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:33668800-33676400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:33668800-33676400	Weak transcription	A549	lung
38	chr6:33669200-33677800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:33669600-33676600	Weak transcription	Hela-S3	cervix
40	chr6:33669800-33676000	Weak transcription	Left Ventricle	heart
41	chr6:33670400-33676200	Weak transcription	HSMM	muscle
42	chr6:33670400-33676400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:33670400-33676600	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:33670400-33677800	Weak transcription	HSMMtube	muscle
45	chr6:33670400-33678000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:33670800-33678200	Weak transcription	NHDF-Ad	bronchial
47	chr6:33671400-33677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:33672000-33676000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:33672000-33677400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:33672200-33677600	Strong transcription	Thymus	Thymus

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