Variant report

Variant	rs6929696
Chromosome Location	chr6:33759290-33759291
allele	C/T
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	BACH1	chr6:33758815-33759365	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33758412..33760501-chr6:33767524..33770306,2	MCF-7	breast:
2	chr6:33758565..33760342-chr6:33771227..33773397,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000096395	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12173787	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190029	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2013365	0.90[AFR][1000 genomes]
rs2281820	0.80[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2296744	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2296746	0.81[AFR][1000 genomes]
rs2296747	0.93[AFR][1000 genomes]
rs2296748	0.82[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2395402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711347	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711349	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713678	0.81[EUR][1000 genomes]
rs4713679	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713681	0.93[AFR][1000 genomes]
rs6457741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751728	0.88[AFR][1000 genomes]
rs7774620	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380378	0.89[AFR][1000 genomes]
rs9394166	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9394167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[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];1.00[ASN][1000 genomes]
rs943471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs943475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[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]
rs943478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6929696	LEMD2	cis	cerebellum	SCAN
rs6929696	PSMB9	cis	lymphoblastoid	seeQTL
rs6929696	LEMD2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757000-33760000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:33757000-33760200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:33757200-33759600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:33757200-33760000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:33757400-33759400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:33757400-33759400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:33757400-33761400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:33757600-33759400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:33757600-33759400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:33757600-33759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:33757600-33759800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:33757600-33760200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:33757600-33760800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:33757600-33761000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:33757600-33762400	Weak transcription	A549	lung
16	chr6:33757600-33763600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
18	chr6:33758000-33760000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:33758000-33762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:33758200-33759400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:33758400-33759400	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:33758400-33763600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:33758800-33760000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:33759000-33760200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:33759000-33761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:33759000-33762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:33759000-33765600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:33759200-33759400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr6:33759200-33759400	Enhancers	Thymus	Thymus
30	chr6:33759200-33759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:33759200-33763600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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