Variant report

Variant	rs4074775
Chromosome Location	chr4:57342122-57342123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57340515..57342236-chr4:57345696..57347786,2	K562	blood:
2	chr4:57333899..57336357-chr4:57340358..57342235,2	MCF-7	breast:
3	chr4:57299376..57303588-chr4:57340719..57344153,5	MCF-7	breast:
4	chr4:57341371..57344122-chr4:57353182..57355439,2	K562	blood:

Variant related genes	Relation type
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1401908	0.90[JPT][hapmap]
rs17086746	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086755	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17086776	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17086786	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17086844	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086924	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292984	0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs28649329	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34228795	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34543011	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796543	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41476944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57439970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58337902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61580407	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61732641	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73155895	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73155901	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73157733	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157739	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73157754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157774	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73159992	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73162272	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73167378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73167396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7437329	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4074775	ARL9	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
4	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:57335800-57354800	Weak transcription	Fetal Heart	heart
8	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:57336000-57342200	Strong transcription	NH-A	brain
14	chr4:57336000-57347600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr4:57336000-57350000	Strong transcription	NHEK	skin
16	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:57336000-57364200	Strong transcription	Osteobl	bone
19	chr4:57336000-57369400	Strong transcription	Liver	Liver
20	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:57336200-57346200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
28	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
29	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:57336400-57342400	Strong transcription	Fetal Intestine Small	intestine
31	chr4:57336400-57342600	Strong transcription	Fetal Stomach	stomach
32	chr4:57336400-57342800	Strong transcription	Brain Germinal Matrix	brain
33	chr4:57336400-57345600	Strong transcription	HUVEC	blood vessel
34	chr4:57336400-57346400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:57336400-57346600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:57336400-57347000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:57336400-57348600	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:57336400-57350000	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:57336600-57360400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:57336600-57364200	Strong transcription	Dnd41	blood
47	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:57336800-57342400	Strong transcription	Primary T cells from cord blood	blood
50	chr4:57337000-57347000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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