Variant report

Variant	rs11126426
Chromosome Location	chr2:74392940-74392941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74391714..74396261-chr2:74424581..74426935,5	MCF-7	breast:
2	chr2:74373575..74375152-chr2:74392686..74395135,2	K562	blood:
3	chr2:74388744..74394878-chr2:74424736..74428064,9	K562	blood:
4	chr2:74056477..74058095-chr2:74392122..74393628,2	MCF-7	breast:
5	chr2:74392325..74394649-chr2:74403053..74406107,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114978	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000163170	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13426653	0.84[ASN][1000 genomes]
rs1620482	0.92[ASW][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1667601	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1667605	0.87[ASN][1000 genomes]
rs1667606	0.91[ASN][1000 genomes]
rs1667609	0.99[ASN][1000 genomes]
rs1723292	0.91[ASN][1000 genomes]
rs34611905	0.84[ASN][1000 genomes]
rs35864597	0.93[ASN][1000 genomes]
rs6546893	0.87[ASN][1000 genomes]
rs6546894	0.85[ASN][1000 genomes]
rs702466	0.93[ASN][1000 genomes]
rs7559252	0.97[ASN][1000 genomes]
rs7562297	0.87[ASN][1000 genomes]
rs8001	0.84[ASN][1000 genomes]
rs828853	0.84[ASN][1000 genomes]
rs828856	0.92[ASN][1000 genomes]
rs828873	0.89[ASN][1000 genomes]
rs828876	0.89[ASN][1000 genomes]
rs828877	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs828882	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs828883	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs828884	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs828885	0.90[ASN][1000 genomes]
rs828886	0.92[ASN][1000 genomes]
rs828888	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs828889	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs828903	0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs844168	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11126426	BOLA3	cis	cerebellum	SCAN
rs11126426	BOLA3	cis	parietal	SCAN
rs11126426	CYP26B1	cis	cerebellum	SCAN
rs11126426	MTHFD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74375800-74403600	Weak transcription	Stomach Mucosa	stomach
2	chr2:74376000-74405000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:74376200-74395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:74376400-74400600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:74376800-74395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:74376800-74397200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:74377200-74400000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:74377400-74400400	Strong transcription	Fetal Thymus	thymus
9	chr2:74377600-74399200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:74377600-74399600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:74377600-74399600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:74377600-74399600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:74377600-74399800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:74377800-74399200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:74377800-74399400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:74377800-74399800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:74377800-74399800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:74377800-74399800	Strong transcription	Placenta	Placenta
19	chr2:74377800-74400000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:74377800-74400200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:74377800-74400200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:74377800-74400400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:74377800-74400400	Strong transcription	A549	lung
24	chr2:74378000-74399200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:74378200-74400400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:74378400-74396400	Strong transcription	Primary B cells from cord blood	blood
27	chr2:74378400-74399200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:74378600-74400400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:74379000-74399600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:74379400-74399600	Strong transcription	Adipose Nuclei	Adipose
31	chr2:74379800-74399800	Strong transcription	Liver	Liver
32	chr2:74380000-74399200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:74380000-74399600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:74380000-74399600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:74380000-74399800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:74380000-74399800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:74380000-74399800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:74380000-74400000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:74380000-74400000	Strong transcription	Osteobl	bone
40	chr2:74380000-74400200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:74380200-74398200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:74380200-74400400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:74380400-74397200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr2:74380400-74398000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:74380600-74399800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:74381000-74399800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:74383000-74399600	Strong transcription	HepG2	liver
48	chr2:74383200-74399800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr2:74383200-74400400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:74383400-74399800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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