Variant report

Variant	rs321623
Chromosome Location	chr4:48024565-48024566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48016518..48018197-chr4:48024501..48026849,2	K562	blood:
2	chr4:47931421..47933962-chr4:48023489..48026018,2	MCF-7	breast:
3	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002500	0.92[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap]
rs10517204	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805163	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10938520	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11733288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504018	0.80[YRI][hapmap]
rs12645245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12651301	0.81[YRI][hapmap]
rs1371729	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs1371732	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1396051	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1440228	0.82[YRI][hapmap]
rs1507913	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1507914	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs178650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837518	0.89[ASN][1000 genomes]
rs1866688	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap]
rs1866689	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs188901	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1899060	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs224800	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2352470	0.85[YRI][hapmap]
rs2581493	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2661513	0.83[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs28578328	0.80[ASN][1000 genomes]
rs28642966	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs28699496	0.82[ASN][1000 genomes]
rs3113881	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113882	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs321621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321633	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321642	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs321644	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321646	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3950558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694880	0.89[CEU][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447603	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs6823184	0.82[YRI][hapmap]
rs6823698	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs6850603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858440	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs7685636	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs978094	0.82[YRI][hapmap]
rs9995122	0.92[ASW][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs321623	CNGA1	cis	Muscle Skeletal	GTEx
rs321623	NFXL1	cis	Whole Blood	GTEx
rs321623	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:48019800-48026600	Weak transcription	NH-A	brain
3	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
4	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
5	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
6	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
7	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:48019800-48034200	Weak transcription	HepG2	liver
9	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
11	chr4:48020000-48026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:48020000-48029200	Weak transcription	GM12878-XiMat	blood
13	chr4:48020400-48027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:48020600-48026200	Weak transcription	Fetal Heart	heart
15	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
16	chr4:48020800-48025000	Enhancers	Fetal Intestine Small	intestine
17	chr4:48020800-48025400	Enhancers	Fetal Intestine Large	intestine
18	chr4:48020800-48026600	Weak transcription	HMEC	breast
19	chr4:48021000-48026400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:48021600-48034200	Weak transcription	Stomach Mucosa	stomach
21	chr4:48021800-48026800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:48022200-48029800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:48022600-48024800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:48022600-48025200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr4:48022600-48026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:48022800-48025600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr4:48022800-48026600	Weak transcription	Gastric	stomach
28	chr4:48022800-48026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:48022800-48029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:48023200-48027000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:48023400-48025000	Enhancers	Duodenum Mucosa	Duodenum
32	chr4:48023400-48026800	Weak transcription	Liver	Liver
33	chr4:48024200-48024600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:48024200-48024600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:48024200-48024600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr4:48024200-48025400	Strong transcription	NHEK	skin
37	chr4:48024400-48024600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:48024400-48024600	Enhancers	Sigmoid Colon	Sigmoid Colon

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