Variant report

Variant	rs3122303
Chromosome Location	chr1:152010087-152010088
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr1:152006830-152010252	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:152001469-152010164	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

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	chr1:152008592..152010631-chr1:153605290..153607916,2	MCF-7	breast:
4	chr1:152008988..152011205-chr1:152060137..152062743,2	MCF-7	breast:
5	chr1:151879656..151883388-chr1:152007614..152010954,7	K562	blood:
6	chr1:151812161..151813920-chr1:152008098..152012154,3	MCF-7	breast:

No data

Variant related genes	Relation type
S100A11	TF binding region
ENSG00000163191	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000182898	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1496037	0.95[ASN][1000 genomes]
rs2999547	0.87[ASN][1000 genomes]
rs2999551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999552	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];1.00[ASN][1000 genomes]
rs2999554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999555	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999562	1.00[ASN][1000 genomes]
rs3007672	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007676	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];1.00[ASN][1000 genomes]
rs3007679	0.87[EUR][1000 genomes]
rs3104205	0.81[ASN][1000 genomes]
rs3122300	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3122302	0.90[EUR][1000 genomes]
rs3122304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3122303	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL
rs3122303	S100A11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152007200-152010200	Active TSS	Gastric	stomach
2	chr1:152009600-152010200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:152009600-152010200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
4	chr1:152009600-152010200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:152009600-152010400	Enhancers	Lung	lung
6	chr1:152009600-152010400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:152009600-152011000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:152009600-152011200	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:152009600-152011400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:152009600-152012000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:152009600-152019800	Weak transcription	Small Intestine	intestine
12	chr1:152009800-152010200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:152009800-152010200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:152009800-152010200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:152009800-152010200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:152009800-152010200	Enhancers	Fetal Lung	lung
17	chr1:152009800-152010200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:152009800-152010400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:152009800-152010400	Enhancers	Placenta	Placenta
20	chr1:152009800-152010400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr1:152009800-152010800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:152009800-152011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:152009800-152011200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:152009800-152011400	Enhancers	Fetal Intestine Large	intestine
25	chr1:152009800-152011400	Enhancers	Fetal Intestine Small	intestine
26	chr1:152009800-152011600	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:152009800-152011600	Enhancers	K562	blood
28	chr1:152009800-152012800	Enhancers	Thymus	Thymus
29	chr1:152009800-152013400	Enhancers	Stomach Mucosa	stomach
30	chr1:152010000-152010200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:152010000-152010200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:152010000-152010200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:152010000-152010200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:152010000-152010200	Enhancers	Colonic Mucosa	Colon
35	chr1:152010000-152010400	Weak transcription	GM12878-XiMat	blood
36	chr1:152010000-152010600	Enhancers	Primary B cells from cord blood	blood
37	chr1:152010000-152010600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:152010000-152011000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:152010000-152011000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:152010000-152011200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:152010000-152011200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:152010000-152011200	Enhancers	Hela-S3	cervix
43	chr1:152010000-152011400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:152010000-152011400	Enhancers	Dnd41	blood
45	chr1:152010000-152011600	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:152010000-152011800	Weak transcription	Esophagus	oesophagus
47	chr1:152010000-152012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:152010000-152013800	Enhancers	Fetal Thymus	thymus
49	chr1:152010000-152016400	Weak transcription	Adipose Nuclei	Adipose
50	chr1:152010000-152017000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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