Variant report

Variant	rs1446556
Chromosome Location	chr6:149637106-149637107
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:149636914-149637128	K562	blood:	n/a	n/a
2	POLR2A	chr6:149636134-149639393	K562	blood:	n/a	n/a
3	IRF1	chr6:149637047-149637127	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149635359..149638022-chr6:149700186..149702826,2	K562	blood:
2	chr6:149637077..149638837-chr6:149727129..149729209,2	K562	blood:
3	chr6:149557890..149560221-chr6:149637001..149638608,2	MCF-7	breast:
4	chr6:149409902..149411675-chr6:149636224..149638635,2	K562	blood:
5	chr6:149406954..149409794-chr6:149636560..149638477,3	MCF-7	breast:
6	chr6:149636797..149639661-chr6:149663144..149666590,3	K562	blood:
7	chr6:149397256..149399835-chr6:149636593..149638648,2	MCF-7	breast:
8	chr6:149619251..149620814-chr6:149634430..149637387,2	K562	blood:
9	chr6:149625453..149629470-chr6:149636058..149640474,5	MCF-7	breast:
10	chr6:149636340..149638301-chr6:150416961..150418644,2	K562	blood:

No data

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000055208	Chromatin interaction
ENSG00000216265	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11155639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[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];0.99[ASN][1000 genomes]
rs11155641	0.87[CHB][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11964335	0.81[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs13219868	0.82[CEU][hapmap]
rs1900300	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs237012	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs237016	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs237019	0.91[CHB][hapmap]
rs237024	0.92[CHB][hapmap]
rs237025	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs237026	0.81[CEU][hapmap];0.93[CHB][hapmap]
rs237028	0.81[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs237035	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs372205	0.80[TSI][hapmap]
rs4895787	0.81[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs6570963	0.81[CEU][hapmap];0.93[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs6570964	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs6922130	0.93[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs6942381	0.92[CHB][hapmap]
rs7752555	0.80[EUR][1000 genomes]
rs7753269	0.80[EUR][1000 genomes]
rs805026	0.82[CEU][hapmap];0.93[CHB][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	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1446556	SUMO4	cis	cerebellum	SCAN
rs1446556	LRP11	cis	cerebellum	SCAN
rs1446556	SHPRH	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149628000-149637800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:149628600-149637200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:149632400-149637200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:149634800-149637200	Weak transcription	K562	blood
5	chr6:149635000-149637200	Weak transcription	Dnd41	blood
6	chr6:149635800-149637400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:149635800-149637400	Weak transcription	Fetal Heart	heart
8	chr6:149636000-149637200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:149636200-149637400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:149636200-149637400	Weak transcription	Fetal Brain Male	brain
11	chr6:149636200-149637400	Weak transcription	Fetal Brain Female	brain
12	chr6:149636600-149637200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:149636600-149637600	Enhancers	Brain Hippocampus Middle	brain
14	chr6:149636600-149637800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:149636600-149637800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:149636800-149637400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:149636800-149637600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:149637000-149637200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:149637000-149637200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:149637000-149637200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:149637000-149637200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:149637000-149637200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:149637000-149637400	Enhancers	Primary B cells from cord blood	blood
24	chr6:149637000-149637400	Enhancers	Primary T cells from cord blood	blood
25	chr6:149637000-149637400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:149637000-149637800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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