Variant report

Variant	rs3957165
Chromosome Location	chr6:33784864-33784865
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33778466..33781199-chr6:33784489..33787096,2	MCF-7	breast:
2	chr6:33784315..33785261-chr6:33864117..33865294,8	MCF-7	breast:
3	chr6:33784287..33785291-chr6:34116957..34117779,3	MCF-7	breast:
4	chr6:33773235..33775828-chr6:33782693..33785367,2	K562	blood:
5	chr6:33784315..33785244-chr6:33864357..33865294,5	MCF-7	breast:
6	chr6:33729702..33730489-chr6:33784415..33785270,3	MCF-7	breast:
7	chr6:33774712..33778330-chr6:33783087..33786924,3	K562	blood:
8	chr6:33776830..33783261-chr6:33784291..33788356,6	K562	blood:
9	chr6:33784583..33786250-chr6:33808935..33810623,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10947436	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10947446	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1536501	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1547668	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs1951930	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998949	0.83[CEU][hapmap]
rs2182659	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2395399	0.80[MKK][hapmap]
rs2395401	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs3998115	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4711350	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4713685	0.80[MKK][hapmap]
rs4713687	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713688	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6915136	1.00[JPT][hapmap]
rs751727	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs942496	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943464	1.00[CHB][hapmap]
rs943472	0.88[CEU][hapmap];1.00[CHB][hapmap]

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	nsv885773	chr6:33778964-33813043	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv885774	chr6:33778964-33840121	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3957165	C6orf125	cis	cerebellum	SCAN
rs3957165	LEMD2	cis	cerebellum	SCAN
rs3957165	BAK1	cis	lymphoblastoid	seeQTL
rs3957165	ZNF76	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33776400-33792400	Weak transcription	Right Atrium	heart
2	chr6:33781800-33792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:33782200-33790600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33782800-33790600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33783800-33787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:33783800-33788200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:33784400-33785400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:33784600-33785400	Enhancers	Fetal Lung	lung
9	chr6:33784800-33785000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr6:33784800-33785000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:33784800-33785000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:33784800-33785000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:33784800-33785000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:33784800-33785400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:33784800-33785600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr6:33784800-33785600	Enhancers	Lung	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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