Variant report

Variant	rs2298059
Chromosome Location	chr6:24426959-24426960
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24426316..24427953-chr6:24428203..24431025,2	MCF-7	breast:
2	chr6:24426425..24428903-chr6:24718888..24721058,2	MCF-7	breast:
3	chr6:24424501..24427723-chr6:24493880..24496586,3	MCF-7	breast:
4	chr6:24421603..24423406-chr6:24425758..24427352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1054862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889240	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889253	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16901722	1.00[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.91[ASN][1000 genomes]
rs17306130	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3469	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]
rs3747771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45448393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45482500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45574139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45590133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461006	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2298059	MRS2	cis	cerebellum	SCAN
rs2298059	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs2298059	HIST1H4I	cis	parietal	SCAN
rs2298059	HIST1H2BA	cis	parietal	SCAN
rs2298059	HIST1H2BG	cis	parietal	SCAN
rs2298059	GPLD1	cis	Esophagus Muscularis	GTEx
rs2298059	ZNF184	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24405000-24427600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:24405400-24427000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:24405400-24427200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:24405400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:24405400-24427600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:24405400-24427600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:24405400-24428200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:24406000-24427000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:24406400-24427600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:24406600-24427400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:24407400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:24407600-24427000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:24407600-24427600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:24407600-24428200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:24407800-24427600	Strong transcription	Fetal Thymus	thymus
17	chr6:24408000-24427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:24409000-24427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:24409200-24427600	Strong transcription	Dnd41	blood
20	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
21	chr6:24412200-24427600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:24412200-24427600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:24412200-24427600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:24412200-24427600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:24412200-24428200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:24412400-24427200	Strong transcription	K562	blood
27	chr6:24412400-24427600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:24412400-24427600	Strong transcription	Fetal Brain Female	brain
29	chr6:24412600-24428600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24412600-24429000	Strong transcription	Primary B cells from cord blood	blood
31	chr6:24412600-24430800	Strong transcription	Primary T cells from cord blood	blood
32	chr6:24412800-24427200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:24413400-24427800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:24413400-24429600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:24416600-24427600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr6:24417400-24427600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:24417400-24451800	Strong transcription	Liver	Liver
38	chr6:24419400-24427200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr6:24420000-24428200	Strong transcription	GM12878-XiMat	blood
40	chr6:24420600-24428800	Weak transcription	Stomach Mucosa	stomach
41	chr6:24420600-24429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:24421200-24428600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:24421200-24428600	Weak transcription	Thymus	Thymus
44	chr6:24421200-24429000	Weak transcription	NHLF	lung
45	chr6:24421200-24448800	Weak transcription	Gastric	stomach
46	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
47	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
48	chr6:24421600-24427000	Weak transcription	Colonic Mucosa	Colon
49	chr6:24421600-24432000	Weak transcription	Fetal Heart	heart
50	chr6:24422400-24429400	Strong transcription	Brain Anterior Caudate	brain

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