Variant report

Variant	rs6824367
Chromosome Location	chr4:77075837-77075838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77067214..77072530-chr4:77074887..77081962,12	K562	blood:
2	chr4:77068526..77071865-chr4:77074983..77079477,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1127705	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12499900	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12641190	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12641529	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12645639	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12646166	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12648162	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12648709	0.95[ASN][1000 genomes]
rs13111705	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13117802	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13119254	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13141802	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1441923	0.96[EUR][1000 genomes]
rs1470191	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1470192	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1470193	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1470194	0.96[EUR][1000 genomes]
rs1550556	0.95[EUR][1000 genomes]
rs17001416	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17001588	0.96[EUR][1000 genomes]
rs17001589	0.96[EUR][1000 genomes]
rs17001604	0.96[EUR][1000 genomes]
rs2034002	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2034003	0.96[EUR][1000 genomes]
rs2053486	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053487	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2304813	0.98[EUR][1000 genomes]
rs2304814	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs28590424	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2869854	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs34022163	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34334700	0.98[EUR][1000 genomes]
rs34974381	0.93[EUR][1000 genomes]
rs34978911	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35583533	1.00[EUR][1000 genomes]
rs35713908	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35783378	0.96[EUR][1000 genomes]
rs36035650	1.00[EUR][1000 genomes]
rs36081173	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796497	0.98[EUR][1000 genomes]
rs3853188	0.96[EUR][1000 genomes]
rs3853189	0.96[EUR][1000 genomes]
rs3853190	0.85[EUR][1000 genomes]
rs3866353	0.96[EUR][1000 genomes]
rs3866354	0.95[EUR][1000 genomes]
rs4452450	0.98[EUR][1000 genomes]
rs4634246	0.98[EUR][1000 genomes]
rs4859425	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4859426	1.00[CEU][hapmap]
rs4859428	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4859617	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4859618	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4859623	0.98[EUR][1000 genomes]
rs4859624	0.98[EUR][1000 genomes]
rs4859625	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4859627	0.96[EUR][1000 genomes]
rs4859628	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4859629	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4859631	0.96[EUR][1000 genomes]
rs59050354	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61153596	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66599877	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs67653006	0.96[EUR][1000 genomes]
rs67917805	0.96[EUR][1000 genomes]
rs6831345	0.87[EUR][1000 genomes]
rs6851995	0.98[EUR][1000 genomes]
rs72857046	0.96[EUR][1000 genomes]
rs72857048	0.96[EUR][1000 genomes]
rs72870920	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7664889	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7673428	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7689378	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7691447	0.96[EUR][1000 genomes]
rs894244	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894247	0.98[EUR][1000 genomes]
rs894248	1.00[CEU][hapmap];0.98[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6824367	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070000-77082600	Weak transcription	Spleen	Spleen
2	chr4:77070200-77081000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:77070200-77082200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:77070200-77082400	Weak transcription	Small Intestine	intestine
5	chr4:77070200-77082600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:77070200-77082600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:77070200-77082600	Weak transcription	Gastric	stomach
8	chr4:77070200-77082800	Weak transcription	Lung	lung
9	chr4:77070400-77077600	Weak transcription	Ovary	ovary
10	chr4:77070400-77079400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:77070400-77081600	Weak transcription	Left Ventricle	heart
12	chr4:77070400-77082000	Weak transcription	Primary B cells from cord blood	blood
13	chr4:77070400-77082200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:77070400-77082200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:77070400-77082600	Weak transcription	Aorta	Aorta
16	chr4:77070400-77093400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:77070600-77077200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:77070600-77078600	Weak transcription	Placenta	Placenta
19	chr4:77070600-77079400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:77070600-77079400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:77070600-77079600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:77070600-77079600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:77070600-77081400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:77070600-77081600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:77070600-77081600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:77070600-77082200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:77070600-77082400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:77070600-77083800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:77070800-77077000	Weak transcription	Fetal Stomach	stomach
31	chr4:77070800-77077400	Weak transcription	HSMM	muscle
32	chr4:77070800-77077600	Weak transcription	Brain Anterior Caudate	brain
33	chr4:77070800-77078000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:77070800-77079400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:77070800-77079600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:77070800-77079600	Weak transcription	Fetal Brain Female	brain
37	chr4:77070800-77079600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:77070800-77080000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:77070800-77080800	Weak transcription	NHDF-Ad	bronchial
40	chr4:77070800-77081400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:77070800-77081400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:77070800-77082000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:77070800-77082200	Weak transcription	Fetal Brain Male	brain
44	chr4:77070800-77082400	Weak transcription	NH-A	brain
45	chr4:77070800-77082600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:77070800-77082600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:77070800-77082600	Weak transcription	A549	lung
48	chr4:77070800-77083000	Weak transcription	Colonic Mucosa	Colon
49	chr4:77070800-77083800	Weak transcription	Fetal Kidney	kidney
50	chr4:77070800-77088400	Weak transcription	Stomach Mucosa	stomach

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