Variant report

Variant	rs4689681
Chromosome Location	chr4:7287579-7287580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7282808..7284476-chr4:7287220..7289819,2	K562	blood:
2	chr4:7282916..7284476-chr4:7287220..7289745,2	K562	blood:
3	chr4:7281415..7283268-chr4:7284765..7287667,2	MCF-7	breast:
4	chr4:7221313..7223378-chr4:7286434..7289285,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10937798	0.86[JPT][hapmap]
rs10937799	0.81[ASN][1000 genomes]
rs11946827	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2336103	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3846421	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs3846422	0.90[ASN][1000 genomes]
rs3857193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3913447	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs3913449	0.81[ASN][1000 genomes]
rs4689680	0.81[ASN][1000 genomes]
rs6823394	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6831675	1.00[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4689681	HTRA3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7278800-7292800	Weak transcription	Right Atrium	heart
2	chr4:7279200-7289400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:7281400-7293200	Weak transcription	Ovary	ovary
4	chr4:7282000-7289800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:7283400-7297000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:7284000-7287600	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:7284400-7289600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:7285200-7287800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7286400-7288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:7287000-7288000	Enhancers	Brain Angular Gyrus	brain
11	chr4:7287000-7288600	Enhancers	Rectal Smooth Muscle	rectum
12	chr4:7287000-7289200	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:7287000-7289200	Enhancers	Fetal Brain Male	brain
14	chr4:7287000-7289400	Enhancers	Brain Anterior Caudate	brain
15	chr4:7287000-7289600	Bivalent Enhancer	Fetal Stomach	stomach
16	chr4:7287000-7290000	Enhancers	Brain Substantia Nigra	brain
17	chr4:7287000-7290000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr4:7287000-7290200	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr4:7287200-7287600	Enhancers	Fetal Brain Female	brain
20	chr4:7287200-7287600	Enhancers	HSMMtube	muscle
21	chr4:7287200-7288200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:7287200-7288200	Enhancers	Brain Germinal Matrix	brain
23	chr4:7287200-7288400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:7287200-7288400	Enhancers	Esophagus	oesophagus
25	chr4:7287200-7290000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr4:7287200-7294400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:7287400-7287600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr4:7287400-7287800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:7287400-7288000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:7287400-7288000	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr4:7287400-7288200	Enhancers	Fetal Lung	lung
32	chr4:7287400-7289200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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