Variant report

Variant	rs192219
Chromosome Location	chr5:40831202-40831203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40795414..40800612-chr5:40826901..40832318,11	MCF-7	breast:
2	chr5:40753095..40762740-chr5:40824814..40831828,21	K562	blood:
3	chr5:40766958..40769662-chr5:40829809..40831566,2	K562	blood:
4	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
5	chr5:40765162..40773094-chr5:40824590..40832435,13	K562	blood:

Variant related genes	Relation type
ENSG00000132356	Chromatin interaction
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10060234	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs1070446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155724	0.90[CEU][hapmap]
rs13167906	0.90[CEU][hapmap]
rs154268	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs154275	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs171605	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs173620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs249414	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs249422	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs249425	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs249428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs249429	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs249437	0.92[ASN][1000 genomes]
rs249441	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257009	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs29742	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29743	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29744	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs29761	1.00[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];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376831	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs381471	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389737	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434778	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs4383756	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs447810	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs457776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461404	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs462366	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6451535	0.90[JPT][hapmap]
rs6897470	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7711806	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs7726237	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs837101	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]

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	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv518711	chr5:40827307-40835627	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	137 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs192219	FBXO4	cis	parietal	SCAN
rs192219		cis	Lymphoblastoid	GTEx
rs192219	RPL37	cis	parietal	SCAN
rs192219	RPL37	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40823600-40833200	Strong transcription	Thymus	Thymus
2	chr5:40824200-40833000	Weak transcription	Fetal Heart	heart
3	chr5:40824200-40833000	Weak transcription	Psoas Muscle	Psoas
4	chr5:40824800-40833000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:40824800-40833200	Strong transcription	Fetal Thymus	thymus
6	chr5:40824800-40833600	Strong transcription	Brain Germinal Matrix	brain
7	chr5:40825000-40832600	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:40825000-40832800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:40825200-40831400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:40825200-40832200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:40825200-40832200	Strong transcription	Liver	Liver
12	chr5:40825200-40832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:40825200-40833200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:40825200-40833400	Strong transcription	Brain Anterior Caudate	brain
15	chr5:40825400-40831400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:40825400-40831800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:40825400-40832000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:40825400-40833800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr5:40825600-40831600	Strong transcription	HMEC	breast
20	chr5:40825600-40831800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:40825600-40831800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr5:40825600-40831800	Strong transcription	NH-A	brain
23	chr5:40825600-40832000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:40825600-40832000	Strong transcription	Osteobl	bone
25	chr5:40825600-40832200	Strong transcription	HSMM	muscle
26	chr5:40825600-40832600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:40825600-40832600	Strong transcription	Fetal Stomach	stomach
28	chr5:40825600-40832600	Strong transcription	Spleen	Spleen
29	chr5:40825600-40832800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:40825600-40833000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr5:40825600-40833200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:40825600-40833200	Strong transcription	Fetal Muscle Leg	muscle
33	chr5:40825600-40833200	Strong transcription	Left Ventricle	heart
34	chr5:40825600-40833400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:40825600-40833400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:40825800-40831800	Strong transcription	Fetal Intestine Small	intestine
37	chr5:40825800-40833200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr5:40826000-40832200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr5:40826000-40833200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:40826000-40833200	Strong transcription	Fetal Brain Female	brain
41	chr5:40826000-40833400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr5:40826000-40833400	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr5:40826200-40832000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:40826200-40832200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:40826200-40833000	Strong transcription	Adipose Nuclei	Adipose
46	chr5:40826400-40831600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:40826400-40831600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:40826400-40831800	Strong transcription	NHEK	skin
49	chr5:40826400-40832000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:40826400-40832000	Strong transcription	NHDF-Ad	bronchial

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