Variant report

Variant	rs11723400
Chromosome Location	chr4:77038473-77038474
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	chr4:77036401..77038944-chr4:77066954..77070829,4	K562	blood:
2	chr4:77037122..77039449-chr4:77042114..77044067,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11097236	0.88[ASN][1000 genomes]
rs11736522	0.80[CEU][hapmap]
rs4241584	0.81[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4288034	0.80[CEU][hapmap]
rs4416502	0.88[ASN][1000 genomes]
rs4538520	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859614	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532203	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6532208	0.80[CEU][hapmap]
rs6829581	0.80[CEU][hapmap]
rs7657598	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11723400	ANXA3	cis	parietal	SCAN
rs11723400	NUP54	cis	Esophagus Muscularis	GTEx
rs11723400	CCDC158	cis	parietal	SCAN
rs11723400	ART3	cis	Nerve Tibial	GTEx
rs11723400	CXCL3	cis	parietal	SCAN
rs11723400	NUP54	cis	parietal	SCAN
rs11723400	CXCL10	cis	parietal	SCAN
rs11723400	NUP54	cis	cerebellum	SCAN
rs11723400	NUP54	cis	Thyroid	GTEx
rs11723400	NUP54	cis	Nerve Tibial	GTEx
rs11723400	ANTXR2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77031600-77039200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:77032800-77039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:77033000-77044800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:77033000-77046800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr4:77033000-77046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:77033200-77038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:77033200-77044400	Weak transcription	Spleen	Spleen
12	chr4:77033200-77045200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:77033200-77045600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr4:77033200-77046200	Strong transcription	Liver	Liver
15	chr4:77033200-77046600	Strong transcription	Fetal Lung	lung
16	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
19	chr4:77033400-77039400	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:77033400-77039800	Strong transcription	HSMM	muscle
21	chr4:77033400-77040600	Weak transcription	Lung	lung
22	chr4:77033400-77041000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:77033400-77041000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:77033400-77041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:77033400-77042200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:77033400-77043400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:77033400-77045600	Strong transcription	Adipose Nuclei	Adipose
28	chr4:77033400-77046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:77033400-77046000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:77033400-77046200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:77033400-77046400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:77033400-77046600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:77033400-77047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:77033400-77048200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:77033400-77052000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:77033400-77052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:77033600-77047600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:77034000-77039400	Strong transcription	Brain Anterior Caudate	brain
44	chr4:77034000-77045600	Strong transcription	Fetal Intestine Large	intestine
45	chr4:77034000-77046200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:77034000-77054000	Strong transcription	Dnd41	blood
47	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:77034200-77039400	Strong transcription	HUVEC	blood vessel
49	chr4:77034200-77039600	Strong transcription	Fetal Kidney	kidney
50	chr4:77034200-77040800	Strong transcription	Osteobl	bone

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