Variant report

Variant	rs1127098
Chromosome Location	chr1:246922390-246922391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:246922317-246922767	HL-60	blood:	n/a	chr1:246922494-246922507 chr1:246922493-246922506 chr1:246922495-246922504 chr1:246922539-246922552 chr1:246922494-246922507
2	SPI1	chr1:246922364-246922582	GM12878	blood:	n/a	chr1:246922494-246922507 chr1:246922493-246922506 chr1:246922495-246922504 chr1:246922539-246922552 chr1:246922494-246922507

No.	Distal block	Cell Line	Cell type
1	chr1:246897250..246899710-chr1:246920316..246922901,2	K562	blood:
2	chr1:246922007..246925353-chr1:246926619..246930863,4	K562	blood:
3	chr1:246809490..246812170-chr1:246921388..246923239,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228879	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1127149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034911	0.81[EUR][1000 genomes]
rs12121187	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12128579	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12129386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12129828	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12402095	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403128	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12407065	0.85[EUR][1000 genomes]
rs12409066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12410595	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735300	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3087781	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34048530	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34677128	0.88[ASN][1000 genomes]
rs35021082	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35570407	0.88[ASN][1000 genomes]
rs35736382	0.88[ASN][1000 genomes]
rs3795469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078128	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41310575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926447	0.89[AMR][1000 genomes]
rs4926449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4926456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61684731	0.90[ASN][1000 genomes]
rs61852479	0.91[ASN][1000 genomes]
rs61852481	0.92[ASN][1000 genomes]
rs61852482	0.92[ASN][1000 genomes]
rs6426329	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6668806	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6682900	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6689579	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6697433	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6697526	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6699332	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6701991	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7365254	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7366187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7410830	0.86[ASN][1000 genomes]
rs74152239	0.97[ASN][1000 genomes]
rs7513496	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs7526237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7528002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7550482	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551836	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9659021	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1127098	CGI-49	cis	multi-tissue	Pritchard
rs1127098	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL
rs1127098	SCCPDH	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
6	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
8	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
10	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:246905000-246923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:246905000-246923800	Weak transcription	Thymus	Thymus
15	chr1:246905000-246924000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
17	chr1:246905600-246923400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:246905600-246923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:246905800-246923800	Weak transcription	Colonic Mucosa	Colon
20	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:246906000-246923800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:246906800-246923000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:246906800-246923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:246907000-246923600	Weak transcription	Aorta	Aorta
25	chr1:246908600-246923400	Weak transcription	NH-A	brain
26	chr1:246908600-246923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:246908800-246922600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:246908800-246922600	Weak transcription	NHLF	lung
29	chr1:246908800-246923000	Weak transcription	HUVEC	blood vessel
30	chr1:246908800-246923600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:246908800-246923600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:246908800-246923800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:246909000-246922400	Weak transcription	Fetal Kidney	kidney
34	chr1:246909000-246922400	Weak transcription	NHDF-Ad	bronchial
35	chr1:246909000-246922600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:246909000-246922600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:246909000-246923600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:246909000-246923600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:246909000-246923800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:246909200-246922400	Weak transcription	Brain Anterior Caudate	brain
41	chr1:246911800-246923400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:246911800-246925000	Weak transcription	Fetal Lung	lung
43	chr1:246912400-246923200	Weak transcription	Lung	lung
44	chr1:246912400-246923600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:246912400-246923800	Weak transcription	Gastric	stomach
46	chr1:246912600-246922600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:246912600-246922800	Weak transcription	Osteobl	bone
48	chr1:246912600-246923400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:246912600-246923600	Weak transcription	Left Ventricle	heart
50	chr1:246912600-246923800	Weak transcription	Ovary	ovary

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