Variant report

Variant	rs6829581
Chromosome Location	chr4:77059130-77059131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77056276..77058049-chr4:77058093..77060100,3	K562	blood:
2	chr4:77058580..77061268-chr4:77061902..77064829,3	MCF-7	breast:
3	chr4:77058522..77060950-chr4:77099295..77101938,2	MCF-7	breast:
4	chr4:77031133..77035310-chr4:77057270..77059295,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11723400	0.80[CEU][hapmap]
rs11734758	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941852	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11946345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108645	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13110133	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126384	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127201	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135639	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241588	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241589	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241590	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4288034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337755	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376175	0.91[AFR][1000 genomes]
rs4498155	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4538520	0.80[CEU][hapmap]
rs4544733	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4552490	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859616	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859620	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532204	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532208	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532244	0.81[AMR][1000 genomes]
rs72655523	0.89[AFR][1000 genomes]
rs735697	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657598	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657823	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675253	0.82[AMR][1000 genomes]
rs9994218	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6829581	NUP54	cis	parietal	SCAN
rs6829581	NUP54	cis	cerebellum	SCAN
rs6829581	ANTXR2	cis	cerebellum	SCAN
rs6829581	PHB	trans	parietal	SCAN
rs6829581	CXCL10	cis	parietal	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	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
5	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:77034400-77067200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:77035200-77062000	Weak transcription	Esophagus	oesophagus
14	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
15	chr4:77035400-77066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
17	chr4:77038200-77062000	Weak transcription	Aorta	Aorta
18	chr4:77039000-77061800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:77039000-77068200	Weak transcription	Psoas Muscle	Psoas
20	chr4:77039000-77068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:77040800-77063200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:77043600-77059400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:77043800-77059800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:77044200-77068200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:77044400-77059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:77044400-77059600	Weak transcription	HSMMtube	muscle
27	chr4:77044400-77062000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:77044600-77061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:77044600-77062000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:77045000-77068600	Weak transcription	Spleen	Spleen
31	chr4:77047000-77063400	Strong transcription	Liver	Liver
32	chr4:77047200-77065600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:77048600-77065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:77048800-77065600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:77049200-77063400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:77049200-77064800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:77049200-77065600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:77050200-77061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:77050200-77068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr4:77050600-77062000	Weak transcription	Fetal Heart	heart
41	chr4:77050800-77059200	Weak transcription	A549	lung
42	chr4:77051000-77061000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:77051400-77064400	Weak transcription	Fetal Intestine Small	intestine
44	chr4:77051400-77065200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:77051400-77066000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:77051400-77068600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:77052200-77059200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:77053400-77065600	Strong transcription	Fetal Thymus	thymus
49	chr4:77053600-77065200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:77053600-77065400	Strong transcription	Fetal Intestine Large	intestine

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