Variant report

Variant	rs520446
Chromosome Location	chr3:43117729-43117730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43115171..43117740-chr3:43120292..43122624,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12233414	1.00[ASW][hapmap];0.84[LWK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs503100	1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs535994	0.89[MKK][hapmap]
rs552472	0.89[MKK][hapmap]
rs574785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630718	1.00[CHD][hapmap]
rs679550	1.00[AFR][1000 genomes];1.00[AMR][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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs520446	IFNGR1	trans	lymphoblastoid	seeQTL
rs520446	IL6R	trans	lymphoblastoid	seeQTL
rs520446	TSPAN1	trans	lymphoblastoid	seeQTL
rs520446	OSBPL10	trans	lymphoblastoid	seeQTL
rs520446	PTK2	trans	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:43102800-43118800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:43104800-43120800	Weak transcription	Gastric	stomach
11	chr3:43105000-43118800	Weak transcription	Thymus	Thymus
12	chr3:43105000-43119600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:43106400-43119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:43106400-43120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43112200-43121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:43112800-43120600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:43113000-43120800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:43114800-43118400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:43115000-43120400	Weak transcription	Fetal Intestine Small	intestine
20	chr3:43115200-43118400	Enhancers	Liver	Liver
21	chr3:43115200-43118400	Weak transcription	Brain Anterior Caudate	brain
22	chr3:43115600-43119000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:43115600-43119600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:43116000-43120800	Weak transcription	Dnd41	blood
25	chr3:43116000-43121000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:43116000-43121000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:43116200-43119400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:43116400-43118800	Weak transcription	Fetal Stomach	stomach
29	chr3:43116600-43119600	Weak transcription	Lung	lung
30	chr3:43117000-43119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:43117000-43119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:43117000-43120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:43117000-43121200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:43117200-43118800	Weak transcription	Fetal Brain Female	brain
35	chr3:43117200-43119000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:43117200-43120200	Weak transcription	Fetal Thymus	thymus
37	chr3:43117200-43120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:43117200-43121000	Weak transcription	Right Ventricle	heart
39	chr3:43117400-43118200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:43117400-43118200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:43117400-43118200	Enhancers	Right Atrium	heart
42	chr3:43117400-43118400	Enhancers	Ovary	ovary
43	chr3:43117400-43119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:43117400-43121000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:43117600-43117800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:43117600-43117800	Enhancers	Esophagus	oesophagus
47	chr3:43117600-43119000	Weak transcription	Aorta	Aorta
48	chr3:43117600-43120000	Weak transcription	Left Ventricle	heart
49	chr3:43117600-43120800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:43117600-43121000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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