Variant report

Variant	rs4243488
Chromosome Location	chr6:149491914-149491915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149491193..149493250-chr6:149500483..149502434,3	MCF-7	breast:
2	chr6:149491339..149493608-chr6:149496512..149499211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263481	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12200486	0.81[ASN][1000 genomes]
rs12212173	0.81[ASN][1000 genomes]
rs12212622	0.81[ASN][1000 genomes]
rs4243487	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897087	0.81[ASN][1000 genomes]
rs6909824	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7743161	0.81[ASN][1000 genomes]
rs9386246	0.86[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	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4243488	MYCT1	cis	cerebellum	SCAN
rs4243488	MAP3K7IP2	cis	multi-tissue	Pritchard
rs4243488	PLEKHG1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149488200-149492000	Weak transcription	Brain Germinal Matrix	brain
2	chr6:149488200-149492400	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:149488600-149492200	Weak transcription	Fetal Heart	heart
4	chr6:149489800-149492800	Enhancers	Liver	Liver
5	chr6:149489800-149492800	Enhancers	GM12878-XiMat	blood
6	chr6:149490000-149492200	Enhancers	Placenta	Placenta
7	chr6:149490000-149492400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:149490200-149492200	Enhancers	HSMM	muscle
9	chr6:149490600-149492800	Enhancers	K562	blood
10	chr6:149490600-149495800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:149490800-149492000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:149490800-149492600	Enhancers	Rectal Smooth Muscle	rectum
13	chr6:149490800-149495800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:149491000-149492000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:149491000-149492200	Enhancers	Fetal Stomach	stomach
16	chr6:149491000-149492400	Enhancers	Adipose Nuclei	Adipose
17	chr6:149491000-149493200	Enhancers	Fetal Lung	lung
18	chr6:149491200-149492200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:149491200-149492400	Bivalent Enhancer	HepG2	liver
20	chr6:149491400-149492000	Weak transcription	Right Atrium	heart
21	chr6:149491400-149492000	Enhancers	Hela-S3	cervix
22	chr6:149491400-149492200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:149491400-149496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:149491600-149492000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:149491800-149492200	Enhancers	Lung	lung
26	chr6:149491800-149492400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:149491800-149492600	Enhancers	Cortex derived primary cultured neurospheres	brain

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