Variant report

Variant	rs3122301
Chromosome Location	chr1:152010725-152010726
allele	A/T
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	POLR2A	chr1:152010427-152011222	HL-60	blood:	n/a	n/a
2	SPI1	chr1:152010713-152010975	GM12878	blood:	n/a	n/a
3	SPI1	chr1:152010602-152011150	HL-60	blood:	n/a	n/a
4	MYC	chr1:152010491-152011262	NB4	blood:	n/a	chr1:152011058-152011073 chr1:152011061-152011072
5	CEBPB	chr1:152010538-152010991	K562	blood:	n/a	chr1:152010594-152010605 chr1:152010592-152010603 chr1:152010549-152010560
6	MAX	chr1:152010455-152011240	NB4	blood:	n/a	chr1:152011058-152011073 chr1:152011061-152011072
7	SPI1	chr1:152010674-152011045	GM12891	blood:	n/a	n/a
8	SPI1	chr1:152010473-152011206	GM12878	blood:	n/a	n/a
9	SPI1	chr1:152010642-152011057	GM12891	blood:	n/a	n/a
10	SPI1	chr1:152010576-152011262	HL-60	blood:	n/a	n/a
11	CEBPB	chr1:152010493-152010926	Hela-S3	cervix:	n/a	chr1:152010594-152010605 chr1:152010592-152010603 chr1:152010549-152010560

No.	Distal block	Cell Line	Cell type
1	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
2	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
3	chr1:152008988..152011205-chr1:152060137..152062743,2	MCF-7	breast:
4	chr1:151879656..151883388-chr1:152007614..152010954,7	K562	blood:
5	chr1:152010384..152012992-chr1:152077475..152079778,2	MCF-7	breast:
6	chr1:151812161..151813920-chr1:152008098..152012154,3	MCF-7	breast:

Variant related genes	Relation type
S100A11	TF binding region
ENSG00000163191	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000182898	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap]
rs10158030	1.00[CHB][hapmap]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888453	1.00[CHB][hapmap]
rs11204911	1.00[CHB][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	0.82[CEU][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1387835	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1490187	1.00[CHB][hapmap]
rs1490191	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1496037	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1552606	1.00[CHB][hapmap]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap]
rs1873311	1.00[CHB][hapmap]
rs1873312	1.00[CHB][hapmap]
rs1967085	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2338018	1.00[CHB][hapmap]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932592	1.00[CHB][hapmap]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999529	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999535	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999538	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999547	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2999551	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2999552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2999554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2999555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999558	1.00[CHB][hapmap]
rs2999562	0.95[ASN][1000 genomes]
rs3001979	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007671	1.00[JPT][hapmap]
rs3007672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007677	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs3007690	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007700	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3122300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122302	0.90[EUR][1000 genomes]
rs3122303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3122304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3134814	1.00[CHB][hapmap]
rs3811422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap]
rs6587629	1.00[CHB][hapmap]
rs6587630	1.00[CHB][hapmap]
rs6587641	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs6659029	1.00[CHB][hapmap]
rs6685291	1.00[CHB][hapmap]
rs6691350	1.00[CHB][hapmap]
rs7529451	1.00[CHB][hapmap]
rs7532721	1.00[CHB][hapmap]
rs902314	1.00[CHB][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9943225	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
5	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3122301	S100A11	Cis_1M	lymphoblastoid	RTeQTL
rs3122301	S100A11	cis	lymphoblastoid	seeQTL
rs3122301	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152009600-152011000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:152009600-152011200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:152009600-152011400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:152009600-152012000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr1:152009600-152019800	Weak transcription	Small Intestine	intestine
6	chr1:152009800-152010800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:152009800-152011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:152009800-152011200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:152009800-152011400	Enhancers	Fetal Intestine Large	intestine
10	chr1:152009800-152011400	Enhancers	Fetal Intestine Small	intestine
11	chr1:152009800-152011600	Enhancers	Duodenum Mucosa	Duodenum
12	chr1:152009800-152011600	Enhancers	K562	blood
13	chr1:152009800-152012800	Enhancers	Thymus	Thymus
14	chr1:152009800-152013400	Enhancers	Stomach Mucosa	stomach
15	chr1:152010000-152011000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:152010000-152011000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:152010000-152011200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:152010000-152011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:152010000-152011200	Enhancers	Hela-S3	cervix
20	chr1:152010000-152011400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:152010000-152011400	Enhancers	Dnd41	blood
22	chr1:152010000-152011600	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:152010000-152011800	Weak transcription	Esophagus	oesophagus
24	chr1:152010000-152012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:152010000-152013800	Enhancers	Fetal Thymus	thymus
26	chr1:152010000-152016400	Weak transcription	Adipose Nuclei	Adipose
27	chr1:152010000-152017000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:152010000-152018400	Weak transcription	A549	lung
29	chr1:152010000-152018400	Weak transcription	NHEK	skin
30	chr1:152010000-152019800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:152010000-152020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:152010200-152014400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:152010200-152016000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:152010200-152020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:152010200-152020000	Weak transcription	Colonic Mucosa	Colon
36	chr1:152010200-152020400	Weak transcription	Gastric	stomach
37	chr1:152010400-152010800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:152010400-152010800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:152010400-152010800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:152010400-152011000	Weak transcription	Placenta	Placenta
41	chr1:152010400-152011200	Enhancers	GM12878-XiMat	blood
42	chr1:152010600-152010800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:152010600-152010800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:152010600-152011200	Enhancers	Fetal Lung	lung
45	chr1:152010600-152011400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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