Variant report

Variant	rs10004377
Chromosome Location	chr4:110648124-110648125
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110642344..110648627-chr4:110649058..110653474,10	K562	blood:
2	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
3	chr4:110629385..110631488-chr4:110647132..110649951,2	K562	blood:
4	chr4:110638419..110640047-chr4:110647082..110649141,2	MCF-7	breast:
5	chr4:110646163..110648808-chr4:110670582..110673028,2	K562	blood:

Variant related genes	Relation type
ENSG00000123739	Chromatin interaction
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11728699	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[YRI][hapmap]
rs11932526	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13107296	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13117504	0.84[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs13127878	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1541373	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17512351	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237056	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301717	0.92[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3087494	0.81[TSI][hapmap]
rs3181187	0.89[ASW][hapmap];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];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796911	0.80[YRI][hapmap]
rs4698780	0.88[LWK][hapmap]
rs4698782	0.83[AFR][1000 genomes]
rs5030534	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5030535	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5030539	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6533444	0.83[LWK][hapmap]
rs6533449	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533451	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831917	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854876	0.89[CEU][hapmap]
rs7439493	0.89[ASW][hapmap];0.88[CEU][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs7674356	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]
rs7682236	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7694620	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];0.97[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992400	0.89[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9995011	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv4463	chr4:110647731-110693125	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10004377	LARP7	cis	parietal	SCAN
rs10004377	CASP6	cis	parietal	SCAN
rs10004377	CASP6	cis	cerebellum	SCAN
rs10004377	RRH	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110625000-110649200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:110625000-110649400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:110625000-110650400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:110625000-110650400	Weak transcription	Spleen	Spleen
5	chr4:110625200-110649200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:110625200-110649200	Weak transcription	NH-A	brain
7	chr4:110625200-110650200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:110625200-110650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:110625400-110648800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:110625400-110649000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:110625400-110649400	Weak transcription	HUVEC	blood vessel
12	chr4:110625800-110648600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:110625800-110648800	Weak transcription	Hela-S3	cervix
14	chr4:110625800-110649400	Weak transcription	Brain Substantia Nigra	brain
15	chr4:110626000-110649600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:110629000-110649200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:110633000-110649000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:110634400-110649200	Weak transcription	Osteobl	bone
19	chr4:110634800-110649200	Weak transcription	Fetal Brain Male	brain
20	chr4:110635000-110650400	Weak transcription	Gastric	stomach
21	chr4:110635400-110650000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:110635600-110649000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:110635800-110648800	Weak transcription	Ovary	ovary
24	chr4:110635800-110648800	Weak transcription	HMEC	breast
25	chr4:110635800-110649800	Weak transcription	Psoas Muscle	Psoas
26	chr4:110635800-110650000	Weak transcription	Right Ventricle	heart
27	chr4:110635800-110650400	Weak transcription	Lung	lung
28	chr4:110638000-110649000	Weak transcription	HSMMtube	muscle
29	chr4:110638200-110649400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:110638200-110649600	Weak transcription	Fetal Brain Female	brain
31	chr4:110638200-110649800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:110638200-110650000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:110638200-110650200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:110638400-110649000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:110638400-110649200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:110638400-110649200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:110638400-110649200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:110638400-110649400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:110638400-110649600	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:110638400-110649600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:110638400-110650000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:110638600-110648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:110638600-110649000	Weak transcription	Dnd41	blood
44	chr4:110638600-110649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:110638600-110649600	Weak transcription	Adipose Nuclei	Adipose
46	chr4:110638600-110649600	Weak transcription	Placenta	Placenta
47	chr4:110638600-110650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:110638600-110650400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:110638800-110648800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:110638800-110648800	Weak transcription	Fetal Intestine Large	intestine

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