Variant report

Variant	rs2814891
Chromosome Location	chr6:38536971-38536972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38535241..38537591-chr6:38552081..38553699,2	MCF-7	breast:
2	chr6:38535111..38538464-chr6:38540181..38544221,3	MCF-7	breast:
3	chr6:38536300..38538310-chr6:38606274..38608039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12525759	0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13219887	0.81[CHD][hapmap]
rs16890826	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16890840	0.83[JPT][hapmap];0.93[MEX][hapmap]
rs1699013	0.94[JPT][hapmap]
rs1699020	0.94[JPT][hapmap]
rs1739625	1.00[JPT][hapmap]
rs1781741	0.89[JPT][hapmap]
rs2748166	0.89[JPT][hapmap]
rs2748168	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2748169	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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814893	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4316001	0.85[CEU][hapmap]
rs62396459	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62399160	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769186	0.83[JPT][hapmap]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2814891	ANKS1A	cis	cerebellum	SCAN
rs2814891	GLO1	cis	parietal	SCAN
rs2814891	ZNF76	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
10	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
12	chr6:38524000-38537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:38532200-38539600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
16	chr6:38532800-38538200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:38533000-38544000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:38533200-38537800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
20	chr6:38534000-38539200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:38534200-38539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
23	chr6:38534400-38544400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:38534800-38537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:38534800-38537800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:38534800-38547000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:38535000-38538200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:38535400-38537600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:38535400-38537800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
32	chr6:38535600-38539000	Weak transcription	HUVEC	blood vessel
33	chr6:38535600-38539200	Weak transcription	GM12878-XiMat	blood
34	chr6:38535600-38543600	Weak transcription	Ovary	ovary
35	chr6:38535600-38543600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:38535600-38544800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:38535600-38547000	Weak transcription	Brain Substantia Nigra	brain
38	chr6:38535600-38547000	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:38535600-38556000	Weak transcription	NHLF	lung
43	chr6:38535600-38557600	Weak transcription	HSMM	muscle
44	chr6:38535800-38539400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:38535800-38539400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:38535800-38543800	Weak transcription	Adipose Nuclei	Adipose
47	chr6:38535800-38544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:38535800-38547800	Weak transcription	Osteobl	bone
49	chr6:38535800-38548000	Weak transcription	Fetal Heart	heart
50	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung

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