Variant report

Variant	rs3818528
Chromosome Location	chr6:33661091-33661092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr6:33660237-33661123	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33660657-33663799	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:33660869-33664890	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:33661033-33661307	HCT-116	colon:	n/a	n/a
5	POLR2A	chr6:33660611-33661892	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr6:33660191-33661295	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
8	ATF2	chr6:33660457-33661143	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:33660850-33661191	HCT-116	colon:	n/a	n/a
10	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
11	POLR2A	chr6:33658928-33664260	K562	blood:	n/a	n/a
12	POLR2A	chr6:33660540-33661951	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr6:33659819-33661962	K562	blood:	n/a	n/a
14	PML	chr6:33660515-33661168	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:33657421-33665985	SK-N-MC	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33587314..33592159-chr6:33656861..33661736,6	K562	blood:
2	chr6:33659672..33661992-chr6:33673865..33675730,2	MCF-7	breast:
3	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
4	chr6:33599796..33602757-chr6:33660954..33662454,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3934	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10672	0.82[CEU][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4713656	0.80[CEU][hapmap]
rs545787	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs764753	0.93[EUR][1000 genomes]
rs9348924	0.84[YRI][hapmap]
rs942642	0.83[EUR][1000 genomes]
rs942643	0.92[YRI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3818528	IHPK3	cis	multi-tissue	Pritchard
rs3818528	LEMD2	cis	cerebellum	SCAN
rs3818528	C6orf125	cis	cerebellum	SCAN
rs3818528	C6orf227	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:33621400-33672600	Strong transcription	Dnd41	blood
3	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr6:33631800-33661200	Weak transcription	Liver	Liver
7	chr6:33636800-33661400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:33637400-33661600	Strong transcription	Esophagus	oesophagus
9	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:33641200-33661600	Strong transcription	NHEK	skin
12	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:33641800-33661800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:33644000-33662000	Weak transcription	Fetal Kidney	kidney
15	chr6:33649800-33661400	Strong transcription	Pancreas	Pancrea
16	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:33652000-33661800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:33653600-33661800	Strong transcription	Hela-S3	cervix
21	chr6:33654600-33661600	Weak transcription	Fetal Brain Female	brain
22	chr6:33654800-33661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:33654800-33662600	Weak transcription	Small Intestine	intestine
24	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
26	chr6:33656400-33661600	Strong transcription	A549	lung
27	chr6:33656400-33662600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
29	chr6:33657000-33661400	Weak transcription	Ovary	ovary
30	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
31	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
33	chr6:33658400-33661800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:33658800-33662600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr6:33659200-33661400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:33659200-33661800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr6:33659200-33665200	Genic enhancers	HMEC	breast
41	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
42	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:33659200-33666600	Enhancers	Right Atrium	heart
44	chr6:33659400-33661800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr6:33659400-33662200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:33659400-33662400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:33659400-33663000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:33659400-33663000	Genic enhancers	NHLF	lung
49	chr6:33659400-33663600	Enhancers	Psoas Muscle	Psoas
50	chr6:33659400-33663800	Enhancers	HSMMtube	muscle

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