Variant report

Variant	rs3087494
Chromosome Location	chr4:110631621-110631622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110630030..110631702-chr4:110772118..110773689,2	MCF-7	breast:
2	chr4:110623524..110627676-chr4:110627933..110634102,8	K562	blood:
3	chr4:110629808..110632372-chr4:110632728..110634458,2	MCF-7	breast:
4	chr4:110614291..110618943-chr4:110630345..110632529,4	K562	blood:
5	chr4:110629777..110633462-chr4:110634208..110638979,5	K562	blood:
6	chr4:110629777..110633985-chr4:110634309..110637022,3	K562	blood:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction
ENSG00000183423	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10004377	0.81[TSI][hapmap]
rs13107296	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13127878	0.94[ASN][1000 genomes]
rs1541373	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1800627	0.82[CEU][hapmap]
rs2237056	0.99[ASN][1000 genomes]
rs2301717	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs3181187	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs5030535	0.81[JPT][hapmap]
rs5030539	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6533448	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533451	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs6812043	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831917	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7674356	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7694620	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs9992400	0.80[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3087494	LRIT3	cis	parietal	SCAN
rs3087494	LARP7	cis	parietal	SCAN
rs3087494	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL
rs3087494	CASP6	cis	cerebellum	SCAN
rs3087494	RRH	cis	cerebellum	SCAN
rs3087494	CASP6	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110624600-110637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:110625000-110632000	Weak transcription	HSMM	muscle
3	chr4:110625000-110632200	Weak transcription	Left Ventricle	heart
4	chr4:110625000-110632600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:110625000-110633800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:110625000-110633800	Weak transcription	Lung	lung
7	chr4:110625000-110634000	Weak transcription	Gastric	stomach
8	chr4:110625000-110634200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:110625000-110634200	Weak transcription	HSMMtube	muscle
10	chr4:110625000-110635400	Weak transcription	Psoas Muscle	Psoas
11	chr4:110625000-110637200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:110625000-110637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:110625000-110638000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:110625000-110638200	Weak transcription	Esophagus	oesophagus
15	chr4:110625000-110640200	Weak transcription	Aorta	Aorta
16	chr4:110625000-110641800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:110625000-110649200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:110625000-110649400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:110625000-110650400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:110625000-110650400	Weak transcription	Spleen	Spleen
21	chr4:110625200-110631800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:110625200-110632000	Weak transcription	Fetal Brain Female	brain
23	chr4:110625200-110632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:110625200-110632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:110625200-110632600	Weak transcription	Brain Anterior Caudate	brain
26	chr4:110625200-110633000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:110625200-110633000	Weak transcription	Right Ventricle	heart
28	chr4:110625200-110634000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:110625200-110634000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:110625200-110634000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:110625200-110634000	Weak transcription	Fetal Brain Male	brain
32	chr4:110625200-110634200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:110625200-110634400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:110625200-110634600	Weak transcription	NHDF-Ad	bronchial
35	chr4:110625200-110635600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:110625200-110637600	Weak transcription	Brain Angular Gyrus	brain
37	chr4:110625200-110637800	Weak transcription	Fetal Thymus	thymus
38	chr4:110625200-110640600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:110625200-110642400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:110625200-110649200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:110625200-110649200	Weak transcription	NH-A	brain
42	chr4:110625200-110650200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:110625200-110650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:110625400-110632400	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:110625400-110632600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:110625400-110632800	Weak transcription	Osteobl	bone
47	chr4:110625400-110633000	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:110625400-110634000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr4:110625400-110634000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:110625400-110634000	Weak transcription	NHEK	skin

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