Variant report

Variant	rs2690059
Chromosome Location	chr6:25353197-25353198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25345654..25347781-chr6:25351220..25353584,2	K562	blood:
2	chr6:25279234..25281745-chr6:25353189..25355641,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1013045	0.96[ASN][1000 genomes]
rs1028347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1209305	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12173289	0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs12210416	0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13217807	0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs1556043	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs169978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs177333	0.81[ASN][1000 genomes]
rs215009	0.85[ASN][1000 genomes]
rs215013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs215014	0.93[ASN][1000 genomes]
rs2254974	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2690094	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2744234	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35361710	0.81[ASN][1000 genomes]
rs4712921	0.88[ASN][1000 genomes]
rs4712922	0.86[ASN][1000 genomes]
rs6456678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760864	1.00[ASW][hapmap];0.84[CEU][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760906	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1792912	chr6:25349637-25354122	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2690059	BTN3A2	cis	cerebellum	SCAN
rs2690059	HIST1H4A	cis	cerebellum	SCAN
rs2690059	HIST1H4A	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
3	chr6:25337400-25357800	Weak transcription	NHEK	skin
4	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
5	chr6:25342800-25354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:25343800-25354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:25347000-25354200	Weak transcription	Stomach Mucosa	stomach
10	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:25349200-25359200	Weak transcription	Ovary	ovary
12	chr6:25349600-25354200	Weak transcription	Aorta	Aorta
13	chr6:25350400-25355200	Enhancers	Fetal Lung	lung
14	chr6:25350600-25356000	Enhancers	Fetal Intestine Large	intestine
15	chr6:25350800-25359200	Weak transcription	Lung	lung
16	chr6:25351000-25359600	Weak transcription	Brain Anterior Caudate	brain
17	chr6:25351200-25353400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:25351200-25354400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:25351200-25357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:25351400-25354200	Weak transcription	Fetal Heart	heart
21	chr6:25351400-25354600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:25351800-25353400	Enhancers	Fetal Intestine Small	intestine
23	chr6:25351800-25353400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:25351800-25359200	Weak transcription	HSMMtube	muscle
25	chr6:25352200-25353200	Enhancers	Primary T cells from cord blood	blood
26	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:25352400-25353200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:25352400-25353200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:25352400-25353200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:25352600-25353200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr6:25352800-25353200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:25352800-25353200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:25352800-25353200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:25352800-25353400	Enhancers	Duodenum Mucosa	Duodenum
35	chr6:25352800-25353400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:25353000-25353400	Enhancers	Small Intestine	intestine
37	chr6:25353000-25354000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:25353000-25359400	Weak transcription	Fetal Thymus	thymus

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