Variant report

Variant	rs6933607
Chromosome Location	chr6:33743997-33743998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33743352..33745913-chr6:33755354..33756938,3	MCF-7	breast:
2	chr6:33738877..33740467-chr6:33741508..33744175,2	K562	blood:
3	chr6:33738877..33741098-chr6:33742637..33744175,2	K562	blood:
4	chr6:33743776..33747465-chr6:33751783..33755243,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1075379	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11753083	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11754690	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]
rs11755593	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757524	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11758463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12524768	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12524835	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887340	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs2281819	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2281820	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2395400	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894342	0.87[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs3763253	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]
rs3828783	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4711346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55775340	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59137082	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61394483	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61662306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910736	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921487	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930201	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6933174	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940353	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72880511	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73412140	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73746509	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs747692	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747693	0.86[CHB][hapmap]
rs751096	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755323	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943461	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943466	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];0.80[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6933607	LEMD2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739000-33746000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
9	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:33740000-33746000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:33740000-33749000	Strong transcription	Brain Anterior Caudate	brain
13	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:33740000-33752800	Strong transcription	Dnd41	blood
17	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:33740000-33753000	Strong transcription	HepG2	liver
19	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:33740200-33744600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr6:33740200-33745800	Strong transcription	Brain Germinal Matrix	brain
24	chr6:33740200-33746600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:33740200-33747800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:33740200-33748400	Weak transcription	Fetal Heart	heart
27	chr6:33740200-33748600	Weak transcription	Right Atrium	heart
28	chr6:33740200-33748800	Strong transcription	Osteobl	bone
29	chr6:33740200-33749200	Strong transcription	Gastric	stomach
30	chr6:33740200-33749400	Strong transcription	Lung	lung
31	chr6:33740200-33750000	Strong transcription	Pancreas	Pancrea
32	chr6:33740200-33751600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
35	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
39	chr6:33740400-33744000	Strong transcription	Brain Angular Gyrus	brain
40	chr6:33740400-33745800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:33740400-33747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:33740400-33747800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr6:33740400-33747800	Strong transcription	Left Ventricle	heart
44	chr6:33740400-33749000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:33740400-33749200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
47	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
49	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:33740600-33744600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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