Variant report

Variant	rs10754532
Chromosome Location	chr1:246888053-246888054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246858802..246860634-chr1:246887473..246889819,2	MCF-7	breast:
2	chr1:246853163..246855096-chr1:246886538..246888986,3	MCF-7	breast:
3	chr1:246852890..246853392-chr1:246887551..246888079,2	K562	blood:
4	chr1:246853196..246855742-chr1:246886661..246889205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10127783	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10159002	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10754533	0.86[CHB][hapmap]
rs10802442	0.88[ASN][1000 genomes]
rs10924820	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10924823	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10924824	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12027222	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12085330	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12090470	0.88[ASN][1000 genomes]
rs12122102	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12132038	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12142760	0.83[ASN][1000 genomes]
rs12144408	0.88[ASN][1000 genomes]
rs3007316	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3007317	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3007318	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3007322	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3007323	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007324	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007411	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34649985	0.88[ASN][1000 genomes]
rs34989088	0.85[ASN][1000 genomes]
rs3795463	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3795464	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3935011	0.83[ASW][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4130316	0.86[ASN][1000 genomes]
rs4130317	0.87[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4244627	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4244630	0.88[ASN][1000 genomes]
rs4926454	0.88[ASN][1000 genomes]
rs4926455	0.87[ASN][1000 genomes]
rs4926457	0.88[ASN][1000 genomes]
rs4926459	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6426323	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs6426326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6426328	0.80[EUR][1000 genomes]
rs6664883	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6685364	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs72764626	0.95[ASN][1000 genomes]
rs7364715	0.94[ASN][1000 genomes]
rs7365076	0.83[ASN][1000 genomes]
rs7366377	0.85[ASN][1000 genomes]
rs7416239	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7532928	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs7532929	0.81[ASN][1000 genomes]
rs9426218	0.93[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9426269	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9426271	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10754532	EFCAB2	cis	parietal	SCAN
rs10754532	SMYD3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246886600-246888400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:246886600-246888400	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr1:246886600-246888400	Active TSS	NHLF	lung
4	chr1:246886600-246888600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:246886600-246889000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:246886800-246888200	Active TSS	Primary T cells from cord blood	blood
7	chr1:246886800-246888200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:246886800-246888200	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr1:246886800-246888400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:246886800-246888400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:246886800-246888400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:246886800-246888400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:246886800-246888400	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:246886800-246888400	Active TSS	Aorta	Aorta
15	chr1:246886800-246888400	Active TSS	Brain Anterior Caudate	brain
16	chr1:246886800-246888400	Active TSS	Brain Cingulate Gyrus	brain
17	chr1:246886800-246888400	Active TSS	Brain Germinal Matrix	brain
18	chr1:246886800-246888400	Active TSS	Stomach Smooth Muscle	stomach
19	chr1:246886800-246888400	Active TSS	A549	lung
20	chr1:246886800-246888400	Active TSS	GM12878-XiMat	blood
21	chr1:246886800-246888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:246886800-246888600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:246886800-246888600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:246886800-246888600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:246886800-246888600	Active TSS	Brain Angular Gyrus	brain
26	chr1:246886800-246888600	Active TSS	Colon Smooth Muscle	Colon
27	chr1:246886800-246888600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:246886800-246888600	Active TSS	Fetal Intestine Large	intestine
29	chr1:246886800-246888600	Active TSS	Fetal Intestine Small	intestine
30	chr1:246886800-246888600	Active TSS	Fetal Stomach	stomach
31	chr1:246886800-246888600	Active TSS	Right Ventricle	heart
32	chr1:246886800-246888800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:246886800-246888800	Active TSS	Brain Substantia Nigra	brain
34	chr1:246886800-246888800	Active TSS	Fetal Brain Female	brain
35	chr1:246886800-246888800	Active TSS	HSMM	muscle
36	chr1:246886800-246888800	Active TSS	K562	blood
37	chr1:246886800-246889000	Active TSS	Duodenum Mucosa	Duodenum
38	chr1:246886800-246889000	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:246886800-246889200	Active TSS	NHDF-Ad	bronchial
40	chr1:246887000-246888200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:246887000-246888200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:246887000-246888200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:246887000-246888200	Active TSS	Brain Hippocampus Middle	brain
44	chr1:246887000-246888200	Active TSS	Fetal Kidney	kidney
45	chr1:246887000-246888200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:246887000-246888200	Active TSS	Thymus	Thymus
47	chr1:246887000-246888200	Active TSS	NH-A	brain
48	chr1:246887000-246888200	Active TSS	Osteobl	bone
49	chr1:246887000-246888400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr1:246887000-246888400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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