Variant report

Variant	rs3763253
Chromosome Location	chr6:33772761-33772762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:33772620-33772770	Caco-2	colon:	n/a	chr6:33772705-33772718
2	CTCF	chr6:33772620-33772770	WERI-Rb-1	eye:	n/a	chr6:33772705-33772718
3	POLR2A	chr6:33769845-33773080	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33771896..33773520-chr6:33777733..33780554,2	MCF-7	breast:
2	chr6:33772133..33773914-chr6:33977490..33979371,2	K562	blood:

Variant related genes	Relation type
MLN	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1075379	0.85[CEU][hapmap];0.80[GIH][hapmap];0.86[EUR][1000 genomes]
rs11753083	0.89[EUR][1000 genomes]
rs11754690	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs11755593	0.87[EUR][1000 genomes]
rs11757524	0.89[EUR][1000 genomes]
rs11758463	0.89[EUR][1000 genomes]
rs12524768	0.87[EUR][1000 genomes]
rs12524835	0.87[EUR][1000 genomes]
rs1887340	0.86[EUR][1000 genomes]
rs2281819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395400	0.94[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2894342	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828783	0.83[CHD][hapmap]
rs4711345	0.85[JPT][hapmap]
rs4711346	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4713677	0.86[JPT][hapmap]
rs55775340	0.88[EUR][1000 genomes]
rs59137082	0.82[EUR][1000 genomes]
rs61394483	0.89[EUR][1000 genomes]
rs61662306	0.89[EUR][1000 genomes]
rs6904716	0.87[JPT][hapmap]
rs6910736	0.82[EUR][1000 genomes]
rs6921487	0.87[EUR][1000 genomes]
rs6930201	0.85[EUR][1000 genomes]
rs6933174	0.89[EUR][1000 genomes]
rs6933568	0.88[EUR][1000 genomes]
rs6933607	0.87[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs6940353	0.89[EUR][1000 genomes]
rs72880511	0.86[EUR][1000 genomes]
rs73412140	0.89[EUR][1000 genomes]
rs73746509	0.87[EUR][1000 genomes]
rs747692	0.94[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs751096	0.89[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs755495	0.94[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs767896	0.93[JPT][hapmap]
rs7755323	0.89[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs943461	0.89[EUR][1000 genomes]
rs943462	0.94[CEU][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs943466	0.94[CEU][hapmap];0.86[EUR][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	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3763253	LEMD2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
2	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33769200-33773200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:33770000-33773000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:33770400-33776000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:33770600-33776200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:33770800-33774400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:33771000-33776200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:33771400-33773200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:33771400-33777000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:33771600-33772800	Enhancers	Fetal Intestine Large	intestine
13	chr6:33771600-33772800	Enhancers	Fetal Intestine Small	intestine
14	chr6:33771600-33774800	Weak transcription	Brain Germinal Matrix	brain
15	chr6:33772000-33772800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:33772200-33775200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:33772400-33775800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:33772400-33776200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:33772600-33775400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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