Variant report

Variant	rs2294345
Chromosome Location	chr6:25606181-25606182
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	MAFK	chr6:25606110-25606222	HepG2	liver:	n/a	n/a
2	MAFK	chr6:25606054-25606189	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25599158..25601193-chr6:25604534..25607048,2	MCF-7	breast:

Variant related genes	Relation type
LRRC16A	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1012898	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];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456324	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10484591	0.89[JPT][hapmap]
rs10946785	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs10946789	0.84[JPT][hapmap]
rs11962024	0.82[ASN][1000 genomes]
rs12213891	0.85[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap]
rs12524760	0.84[JPT][hapmap]
rs12525376	0.84[JPT][hapmap]
rs12528182	0.84[JPT][hapmap]
rs12529390	0.84[JPT][hapmap]
rs1406927	0.86[JPT][hapmap]
rs150551	0.89[JPT][hapmap]
rs1569483	0.82[ASN][1000 genomes]
rs1883260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1883261	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1997672	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2064126	0.83[JPT][hapmap]
rs2064127	0.84[JPT][hapmap]
rs2072846	0.84[JPT][hapmap]
rs2072847	0.84[JPT][hapmap]
rs2072851	0.84[JPT][hapmap]
rs2077393	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2328890	0.84[JPT][hapmap]
rs3788991	0.89[GIH][hapmap]
rs3804105	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3804106	0.85[ASN][1000 genomes]
rs3804108	0.85[ASN][1000 genomes]
rs3804109	0.84[ASN][1000 genomes]
rs3804111	0.95[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804112	0.80[JPT][hapmap]
rs3804113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804118	0.89[JPT][hapmap]
rs3827500	0.85[ASN][1000 genomes]
rs4140640	0.84[JPT][hapmap]
rs4711088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712952	0.89[JPT][hapmap]
rs4712953	0.84[JPT][hapmap]
rs4712954	0.84[JPT][hapmap]
rs59606579	0.85[ASN][1000 genomes]
rs6903765	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6903817	0.82[ASN][1000 genomes]
rs6904044	0.82[ASN][1000 genomes]
rs6908390	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7383628	0.84[ASN][1000 genomes]
rs742131	0.80[CHB][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742132	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7746950	0.88[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7754155	0.84[JPT][hapmap]
rs7761700	0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7775000	0.84[JPT][hapmap]
rs9295666	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9467552	0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2294345	HIST1H3B	cis	cerebellum	SCAN
rs2294345	TRIM38	cis	cerebellum	SCAN
rs2294345	SCGN	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25516800-25606400	Weak transcription	Lung	lung
2	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
4	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
5	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
6	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
9	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
14	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
16	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:25589200-25623400	Weak transcription	HMEC	breast
18	chr6:25590800-25618000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:25592400-25625600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:25593200-25608800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:25593400-25609600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:25593600-25618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:25594200-25629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:25594400-25618200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:25594400-25627200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:25594600-25606400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:25594600-25607200	Weak transcription	Aorta	Aorta
28	chr6:25594600-25627200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:25594600-25629600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:25594800-25624600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:25595000-25626800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:25595000-25627000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:25595200-25610400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:25595600-25618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:25595800-25610200	Weak transcription	Ovary	ovary
36	chr6:25596000-25606400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:25596200-25609800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:25597800-25607800	Weak transcription	Spleen	Spleen
39	chr6:25597800-25610800	Weak transcription	Left Ventricle	heart
40	chr6:25598000-25610400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:25598000-25622800	Weak transcription	Gastric	stomach
42	chr6:25599200-25622800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:25599400-25618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:25600600-25612400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:25601000-25612200	Weak transcription	Placenta	Placenta
46	chr6:25601000-25619400	Weak transcription	Fetal Stomach	stomach
47	chr6:25601200-25612000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:25601400-25606400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:25601400-25608800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:25601600-25626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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