Variant report

Variant	rs7677409
Chromosome Location	chr4:149268752-149268753
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11099694	0.90[YRI][hapmap]
rs12331046	0.82[AFR][1000 genomes]
rs1512331	0.87[MKK][hapmap]
rs1512333	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1512336	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2063557	0.88[AFR][1000 genomes]
rs2137332	1.00[ASW][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4835137	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57841317	1.00[AMR][1000 genomes]
rs59379699	1.00[AMR][1000 genomes]
rs6825048	0.82[ASW][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap]
rs72655278	1.00[AMR][1000 genomes]
rs7438918	0.90[YRI][hapmap]
rs993386	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1031815	chr4:149172485-149282928	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1028105	chr4:149199913-149284620	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv537297	chr4:149199913-149284620	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1016966	chr4:149209467-149341037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1019350	chr4:149232430-149282117	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3584816	chr4:149254670-149293317	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7677409	NPLOC4	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149249400-149271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr4:149266000-149276400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:149267000-149280600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:149267200-149269400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:149267200-149276800	Weak transcription	Colonic Mucosa	Colon
6	chr4:149267400-149276800	Weak transcription	Liver	Liver
7	chr4:149267600-149269800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:149267600-149272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:149267600-149276600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:149267600-149276600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:149267800-149271400	Weak transcription	Psoas Muscle	Psoas
12	chr4:149267800-149282000	Weak transcription	Right Ventricle	heart
13	chr4:149268200-149269200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:149268200-149276200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:149268200-149276600	Weak transcription	Left Ventricle	heart
16	chr4:149268200-149276600	Weak transcription	Ovary	ovary
17	chr4:149268200-149276600	Weak transcription	Right Atrium	heart
18	chr4:149268200-149288000	Weak transcription	Small Intestine	intestine
19	chr4:149268400-149269200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:149268400-149270400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:149268600-149268800	Enhancers	Rectal Mucosa Donor 29	rectum

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