Variant report

Variant	rs9396554
Chromosome Location	chr6:15074526-15074527
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15070190..15074230-chr6:15074491..15076843,3	MCF-7	breast:
2	chr6:15062551..15066335-chr6:15072410..15076511,4	MCF-7	breast:
3	chr6:15072178..15075145-chr6:15244379..15247154,3	K562	blood:
4	chr6:15065231..15078374-chr6:15243362..15252213,26	MCF-7	breast:
5	chr6:15070915..15075463-chr6:15246209..15249841,5	MCF-7	breast:
6	chr6:15065449..15068780-chr6:15072645..15074662,4	K562	blood:
7	chr6:15069299..15075541-chr6:15075577..15080851,9	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000271888	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16876061	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6928159	1.00[CEU][hapmap]
rs6928936	1.00[CEU][hapmap]
rs72832873	0.92[EUR][1000 genomes]
rs72832876	0.92[EUR][1000 genomes]
rs9349965	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9358050	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs9370791	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383017	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9396553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9396555	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9396556	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883454	chr6:15009137-15081252	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9396554	BBC3	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15043800-15077400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:15067200-15076600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:15067400-15076600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:15067600-15076200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:15068800-15077200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:15069200-15076400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:15072600-15075600	Weak transcription	K562	blood
8	chr6:15073200-15075600	Enhancers	Brain Cingulate Gyrus	brain
9	chr6:15073600-15074600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr6:15073600-15074800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:15073600-15075400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:15073600-15075400	Enhancers	Brain Anterior Caudate	brain
13	chr6:15073600-15076600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:15073800-15075000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:15073800-15079600	Weak transcription	Stomach Mucosa	stomach
16	chr6:15074000-15075200	Weak transcription	Placenta	Placenta
17	chr6:15074000-15076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:15074000-15076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:15074000-15077400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:15074200-15075600	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:15074400-15075400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:15074400-15076400	Weak transcription	GM12878-XiMat	blood
23	chr6:15074400-15076600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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