Variant report

Variant	rs322410
Chromosome Location	chr4:187809027-187809028
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	GATA3	chr4:187808615-187809037	SK-N-SH	brain:	n/a	chr4:187808909-187808918 chr4:187808734-187808744
2	JUND	chr4:187809024-187809030	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:187765177..187771006-chr4:187807000..187811310,9	K562	blood:
2	chr4:187802654..187805623-chr4:187805996..187810287,4	K562	blood:
3	chr4:187768429..187770069-chr4:187807061..187809339,2	K562	blood:
4	chr4:187637189..187639429-chr4:187808650..187810594,2	K562	blood:

Variant related genes	Relation type
ENSG00000272218	TF binding region
ENSG00000250829	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11132415	1.00[ASN][1000 genomes]
rs11132416	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1431927	0.84[ASN][1000 genomes]
rs167721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1835748	0.84[ASN][1000 genomes]
rs2241672	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs322412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429509	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443846	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4861728	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4862740	0.93[EUR][1000 genomes]
rs4862741	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58176956	0.95[ASN][1000 genomes]
rs59618202	0.83[ASN][1000 genomes]
rs60226958	0.83[ASN][1000 genomes]
rs60326187	0.95[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	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
9	nsv1031603	chr4:187636716-188020741	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv880401	chr4:187668795-188047143	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1015893	chr4:187768295-188338413	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv537441	chr4:187768295-188338413	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv525720	chr4:187792665-188426129	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs322410	TLR3	cis	parietal	SCAN
rs322410	CASP3	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187804000-187812400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:187807000-187809400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:187807600-187809200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:187807800-187809400	Flanking Active TSS	NHEK	skin
5	chr4:187807800-187809600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:187808000-187809400	Enhancers	Fetal Kidney	kidney
7	chr4:187808200-187809200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:187808200-187809400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:187808200-187809400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:187808200-187809400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:187808200-187809400	Enhancers	NH-A	brain
12	chr4:187808200-187809600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:187808200-187809800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:187808200-187821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:187808400-187809200	Enhancers	Fetal Brain Female	brain
16	chr4:187808400-187809200	Enhancers	Fetal Lung	lung
17	chr4:187808600-187809200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:187808600-187809600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:187808800-187809400	Enhancers	Brain Germinal Matrix	brain
20	chr4:187808800-187809600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:187808800-187811200	Active TSS	K562	blood
22	chr4:187809000-187809200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:187809000-187809200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr4:187809000-187809200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:187809000-187809200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:187809000-187809400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:187809000-187809400	Enhancers	HMEC	breast
28	chr4:187809000-187809600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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