Variant report

Variant	rs2395401
Chromosome Location	chr6:33759471-33759472
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	POLR2A	chr6:33759449-33759566	MCF10A-Er-Src	breast:	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: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10755683	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10947428	0.84[CEU][hapmap]
rs10947436	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947446	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes]
rs11751943	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318691	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1536500	0.91[EUR][1000 genomes]
rs1536501	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547668	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951930	0.80[AFR][1000 genomes]
rs1998949	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2182658	0.85[ASW][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2182659	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395446	0.88[EUR][1000 genomes]
rs2395447	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs3957165	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4711350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713676	0.83[EUR][1000 genomes]
rs4713685	0.85[ASW][hapmap]
rs4713687	0.82[AFR][1000 genomes]
rs4713688	0.82[AFR][1000 genomes]
rs487835	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.88[EUR][1000 genomes]
rs4996879	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs530614	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549652	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs570749	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs602399	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs652049	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs680608	0.94[ASN][1000 genomes]
rs684119	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs688209	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6921772	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7449707	0.82[EUR][1000 genomes]
rs751727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756138	0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs756139	0.85[ASW][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs791904	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9380379	0.86[EUR][1000 genomes]
rs942496	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs943463	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943465	0.86[EUR][1000 genomes]
rs943472	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943473	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs943476	0.92[ASW][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9461905	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9461907	0.92[EUR][1000 genomes]
rs9469542	1.00[JPT][hapmap]

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
rs2395401	RXRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2395401	BAK1	cis	Skin Sun Exposed Lower leg	GTEx
rs2395401	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr6:33757400-33761400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:33757600-33759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:33757600-33759800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:33757600-33760200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:33757600-33760800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:33757600-33761000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:33757600-33762400	Weak transcription	A549	lung
12	chr6:33757600-33763600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
14	chr6:33758000-33760000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:33758000-33762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:33758400-33763600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:33758800-33760000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:33759000-33760200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:33759000-33761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:33759000-33762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:33759000-33765600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:33759200-33759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:33759200-33763600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:33759400-33759800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:33759400-33760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:33759400-33761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:33759400-33762200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:33759400-33762600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:33759400-33762600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:33759400-33762800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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