Variant report

Variant	rs7674356
Chromosome Location	chr4:110632195-110632196
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110623524..110627676-chr4:110627933..110634102,8	K562	blood:
2	chr4:110629808..110632372-chr4:110632728..110634458,2	MCF-7	breast:
3	chr4:110614291..110618943-chr4:110630345..110632529,4	K562	blood:
4	chr4:110629777..110633462-chr4:110634208..110638979,5	K562	blood:
5	chr4:110623428..110625453-chr4:110631724..110634385,2	MCF-7	breast:
6	chr4:110629777..110633985-chr4:110634309..110637022,3	K562	blood:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10004377	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11728699	0.89[ASW][hapmap];0.85[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs11932526	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107296	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13117504	0.83[YRI][hapmap]
rs13127878	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1541373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512351	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237056	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2301717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087494	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs3181187	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698780	0.88[LWK][hapmap]
rs4698782	0.86[AFR][1000 genomes]
rs5030534	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5030535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030539	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6533444	0.83[LWK][hapmap]
rs6533449	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6831917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6854876	0.82[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs7439493	0.89[ASW][hapmap];0.80[CEU][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs7682236	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992400	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995011	0.89[ASW][hapmap];0.85[CEU][hapmap];0.91[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7674356	CASP6	cis	cerebellum	SCAN
rs7674356	CASP6	cis	parietal	SCAN
rs7674356	RRH	cis	cerebellum	SCAN
rs7674356	LARP7	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	chr4:110625000-110632200	Weak transcription	Left Ventricle	heart
3	chr4:110625000-110632600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:110625000-110633800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:110625000-110633800	Weak transcription	Lung	lung
6	chr4:110625000-110634000	Weak transcription	Gastric	stomach
7	chr4:110625000-110634200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:110625000-110634200	Weak transcription	HSMMtube	muscle
9	chr4:110625000-110635400	Weak transcription	Psoas Muscle	Psoas
10	chr4:110625000-110637200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:110625000-110637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:110625000-110638000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:110625000-110638200	Weak transcription	Esophagus	oesophagus
14	chr4:110625000-110640200	Weak transcription	Aorta	Aorta
15	chr4:110625000-110641800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:110625000-110649200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:110625000-110649400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:110625000-110650400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:110625000-110650400	Weak transcription	Spleen	Spleen
20	chr4:110625200-110632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:110625200-110632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:110625200-110632600	Weak transcription	Brain Anterior Caudate	brain
23	chr4:110625200-110633000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:110625200-110633000	Weak transcription	Right Ventricle	heart
25	chr4:110625200-110634000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:110625200-110634000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:110625200-110634000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:110625200-110634000	Weak transcription	Fetal Brain Male	brain
29	chr4:110625200-110634200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:110625200-110634400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:110625200-110634600	Weak transcription	NHDF-Ad	bronchial
32	chr4:110625200-110635600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:110625200-110637600	Weak transcription	Brain Angular Gyrus	brain
34	chr4:110625200-110637800	Weak transcription	Fetal Thymus	thymus
35	chr4:110625200-110640600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:110625200-110642400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:110625200-110649200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:110625200-110649200	Weak transcription	NH-A	brain
39	chr4:110625200-110650200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:110625200-110650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:110625400-110632400	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:110625400-110632600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:110625400-110632800	Weak transcription	Osteobl	bone
44	chr4:110625400-110633000	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:110625400-110634000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:110625400-110634000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:110625400-110634000	Weak transcription	NHEK	skin
48	chr4:110625400-110634600	Weak transcription	Brain Germinal Matrix	brain
49	chr4:110625400-110634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:110625400-110636800	Weak transcription	NHLF	lung

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