Variant report

Variant	rs2182658
Chromosome Location	chr6:33748831-33748832
allele	G/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	POLR2A	chr6:33748785-33749736	HUVEC	blood vessel:	n/a	n/a
2	EP300	chr6:33748809-33750016	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr6:33748743-33749970	ECC-1	luminal epithelium:	n/a	n/a
4	TCF7L2	chr6:33748715-33749914	PANC-1	pancreas:	n/a	n/a
5	TEAD4	chr6:33748730-33749936	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr6:33748737-33749981	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr6:33748677-33750103	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:33748700-33750816	K562	blood:	n/a	n/a
9	NFIC	chr6:33748809-33749841	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33746735..33748851-chr6:33749721..33751563,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10755683	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947436	0.85[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs11751943	0.87[EUR][1000 genomes]
rs1318691	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536500	0.82[EUR][1000 genomes]
rs1536501	0.92[ASW][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs1547668	0.84[YRI][hapmap]
rs1998949	0.82[EUR][1000 genomes]
rs2182659	0.85[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2395399	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2395401	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]
rs2395446	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395447	0.88[EUR][1000 genomes]
rs4711350	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4713676	0.87[EUR][1000 genomes]
rs4713685	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4996879	0.83[EUR][1000 genomes]
rs530614	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs545787	1.00[JPT][hapmap]
rs568901	0.82[JPT][hapmap]
rs602399	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs652049	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs6921772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449707	0.86[EUR][1000 genomes]
rs751727	0.84[YRI][hapmap];0.88[EUR][1000 genomes]
rs756138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752348	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380379	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs942496	0.81[YRI][hapmap]
rs943464	0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs943465	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs943472	0.85[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs943473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461905	0.82[EUR][1000 genomes]
rs9461907	0.82[EUR][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
rs2182658	C6orf125	cis	parietal	SCAN
rs2182658	BAK1	cis	lymphoblastoid	seeQTL
rs2182658	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:33740000-33749000	Strong transcription	Brain Anterior Caudate	brain
11	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:33740000-33752800	Strong transcription	Dnd41	blood
15	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:33740000-33753000	Strong transcription	HepG2	liver
17	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:33740200-33749200	Strong transcription	Gastric	stomach
21	chr6:33740200-33749400	Strong transcription	Lung	lung
22	chr6:33740200-33750000	Strong transcription	Pancreas	Pancrea
23	chr6:33740200-33751600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
26	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
30	chr6:33740400-33749000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:33740400-33749200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
33	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
35	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:33740600-33749000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:33740600-33749200	Strong transcription	Adipose Nuclei	Adipose
38	chr6:33740600-33753000	Strong transcription	Liver	Liver
39	chr6:33740600-33753000	Strong transcription	Colonic Mucosa	Colon
40	chr6:33740600-33754200	Strong transcription	Fetal Intestine Large	intestine
41	chr6:33740600-33754200	Strong transcription	Fetal Intestine Small	intestine
42	chr6:33740800-33749200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:33741000-33749000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:33741000-33749000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:33741000-33751600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:33741000-33752600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr6:33741000-33753000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:33741000-33753200	Strong transcription	Fetal Brain Female	brain
49	chr6:33741000-33754000	Strong transcription	Fetal Thymus	thymus
50	chr6:33741400-33749000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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