Variant report

Variant	rs3122300
Chromosome Location	chr1:152012386-152012387
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	CCNT2	chr1:152012309-152012774	K562	blood:	n/a	n/a

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	chr1:152010384..152012992-chr1:152077475..152079778,2	MCF-7	breast:
4	chr1:152012090..152014463-chr17:57922085..57923933,2	MCF-7	breast:

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

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

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]
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	1.00[JPT][hapmap]
rs2999550	0.90[ASN][1000 genomes]
rs2999551	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]
rs2999552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999553	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999554	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999555	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[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999558	1.00[CHB][hapmap]
rs2999559	0.91[ASN][1000 genomes]
rs3001979	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007671	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3007672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007673	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007674	0.97[ASN][1000 genomes]
rs3007676	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007678	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];0.94[ASN][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]
rs3122301	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];0.91[ASN][1000 genomes]
rs3122303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122304	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3134814	1.00[CHB][hapmap]
rs3811422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3122300	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL
rs3122300	S100A11	Cis_1M	lymphoblastoid	RTeQTL
rs3122300	S100A11	cis	multi-tissue	Pritchard
rs3122300	S100A11	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152009600-152019800	Weak transcription	Small Intestine	intestine
2	chr1:152009800-152012800	Enhancers	Thymus	Thymus
3	chr1:152009800-152013400	Enhancers	Stomach Mucosa	stomach
4	chr1:152010000-152013800	Enhancers	Fetal Thymus	thymus
5	chr1:152010000-152016400	Weak transcription	Adipose Nuclei	Adipose
6	chr1:152010000-152017000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:152010000-152018400	Weak transcription	A549	lung
8	chr1:152010000-152018400	Weak transcription	NHEK	skin
9	chr1:152010000-152019800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:152010000-152020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:152010200-152014400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:152010200-152016000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:152010200-152020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:152010200-152020000	Weak transcription	Colonic Mucosa	Colon
15	chr1:152010200-152020400	Weak transcription	Gastric	stomach
16	chr1:152010800-152018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:152011200-152013600	Enhancers	Primary B cells from cord blood	blood
18	chr1:152011200-152016400	Weak transcription	Hela-S3	cervix
19	chr1:152011400-152012400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:152011400-152012400	Weak transcription	Fetal Intestine Small	intestine
21	chr1:152011400-152012600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:152011400-152019600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:152011800-152013000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:152012000-152012400	Weak transcription	Esophagus	oesophagus
25	chr1:152012000-152012800	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:152012000-152013200	Enhancers	K562	blood
27	chr1:152012000-152015200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:152012200-152012400	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:152012200-152012600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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