Variant report

Variant	rs3846424
Chromosome Location	chr4:7292894-7292895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7214030..7216634-chr4:7290499..7293149,2	MCF-7	breast:
2	chr4:7194014..7196749-chr4:7291748..7294581,2	MCF-7	breast:
3	chr4:7288760..7290651-chr4:7292846..7295423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184985	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11946827	0.86[TSI][hapmap]
rs2336103	0.83[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3846421	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3846422	0.93[EUR][1000 genomes]
rs3913447	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs6814319	0.81[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	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv829850	chr4:7112509-7314016	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv432556	chr4:7174993-7391948	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv878541	chr4:7211197-7341243	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv461200	chr4:7256620-7297506	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv593567	chr4:7256620-7297506	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv461201	chr4:7256620-7311399	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv593568	chr4:7256620-7311399	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878543	chr4:7282506-7353052	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv878544	chr4:7285356-7359966	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv878545	chr4:7285356-7363007	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv878546	chr4:7285356-7376694	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv878547	chr4:7289113-7376694	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3846424	HTRA3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7281400-7293200	Weak transcription	Ovary	ovary
2	chr4:7283400-7297000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7287200-7294400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:7287600-7293400	Weak transcription	Fetal Brain Female	brain
5	chr4:7288000-7293400	Weak transcription	Brain Angular Gyrus	brain
6	chr4:7288200-7293200	Weak transcription	Fetal Lung	lung
7	chr4:7288800-7294000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:7289200-7293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:7289200-7296800	Weak transcription	Fetal Brain Male	brain
10	chr4:7290000-7293000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:7290400-7296400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:7291600-7297000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:7291800-7293000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:7291800-7294200	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:7291800-7297200	Weak transcription	Liver	Liver
16	chr4:7292000-7293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:7292000-7293000	Weak transcription	Fetal Stomach	stomach
18	chr4:7292400-7293800	Enhancers	Gastric	stomach
19	chr4:7292600-7293800	Enhancers	Colon Smooth Muscle	Colon
20	chr4:7292600-7293800	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr4:7292800-7293400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:7292800-7293800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:7292800-7293800	Enhancers	Esophagus	oesophagus
24	chr4:7292800-7293800	Enhancers	Right Atrium	heart
25	chr4:7292800-7293800	Enhancers	Stomach Smooth Muscle	stomach
26	chr4:7292800-7294000	Enhancers	Brain Anterior Caudate	brain
27	chr4:7292800-7294000	Enhancers	Left Ventricle	heart
28	chr4:7292800-7294200	Enhancers	Brain Germinal Matrix	brain
29	chr4:7292800-7294200	Enhancers	Right Ventricle	heart
30	chr4:7292800-7294800	Enhancers	Brain Hippocampus Middle	brain

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