Variant report

Variant	rs1381462
Chromosome Location	chr3:158518963-158518964
allele	C/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	chr3:158518843-158520542	IMR90	lung:	n/a	n/a
2	HA-E2F1	chr3:158518788-158520590	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:158518862-158520256	U87	brain:	n/a	n/a
4	POLR2A	chr3:158518781-158520577	K562	blood:	n/a	n/a
5	HCFC1	chr3:158518599-158520668	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr3:158518622-158520812	IMR90	lung:	n/a	chr3:158520438-158520447
7	MXI1	chr3:158518465-158521051	SK-N-SH	brain:	n/a	chr3:158520438-158520447
8	POLR2A	chr3:158518930-158520383	K562	blood:	n/a	n/a
9	POLR2A	chr3:158518706-158520289	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr3:158518904-158519264	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr3:158518777-158520256	U87	brain:	n/a	n/a
12	POLR2A	chr3:158518860-158520344	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158360988..158362549-chr3:158517154..158519715,2	K562	blood:

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1381464	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985781	0.84[ASN][1000 genomes]
rs3755746	0.83[AMR][1000 genomes]
rs3816637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4680466	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56070013	0.96[ASN][1000 genomes]
rs73158358	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7617706	0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs9290028	0.83[AMR][1000 genomes]
rs9810241	0.84[AMR][1000 genomes]
rs9859969	0.96[ASN][1000 genomes]
rs9861289	0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs9861622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1381462	IL12A	cis	parietal	SCAN
rs1381462	LXN	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158509200-158519000	Weak transcription	Aorta	Aorta
2	chr3:158509200-158519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:158517400-158519000	Weak transcription	Hela-S3	cervix
4	chr3:158518200-158519000	Enhancers	K562	blood
5	chr3:158518400-158519000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:158518400-158519400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:158518600-158519000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:158518600-158519000	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:158518600-158519000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:158518600-158519000	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr3:158518600-158519000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:158518600-158519000	Enhancers	HMEC	breast
13	chr3:158518600-158519200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr3:158518600-158519200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:158518600-158519200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:158518600-158519200	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr3:158518600-158519400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:158518600-158519400	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr3:158518600-158519400	Flanking Active TSS	NHEK	skin
20	chr3:158518600-158519400	Flanking Active TSS	Osteobl	bone
21	chr3:158518600-158519600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:158518600-158519600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:158518600-158519600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:158518600-158520200	Active TSS	Brain Anterior Caudate	brain
25	chr3:158518600-158520600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:158518600-158521400	Active TSS	Brain Cingulate Gyrus	brain
27	chr3:158518800-158519000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr3:158518800-158519000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:158518800-158519000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:158518800-158519000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:158518800-158519000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:158518800-158519000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr3:158518800-158519000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
34	chr3:158518800-158519000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:158518800-158519000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:158518800-158519000	Enhancers	Primary B cells from cord blood	blood
37	chr3:158518800-158519000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:158518800-158519000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:158518800-158519000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:158518800-158519000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:158518800-158519000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:158518800-158519000	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr3:158518800-158519000	Flanking Active TSS	Esophagus	oesophagus
44	chr3:158518800-158519000	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr3:158518800-158519000	Active TSS	Fetal Kidney	kidney
46	chr3:158518800-158519000	Bivalent Enhancer	Fetal Thymus	thymus
47	chr3:158518800-158519000	Enhancers	Lung	lung
48	chr3:158518800-158519000	Active TSS	Right Atrium	heart
49	chr3:158518800-158519000	Flanking Active TSS	HepG2	liver
50	chr3:158518800-158519000	Enhancers	HSMMtube	muscle

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