Variant report

Variant	rs6855619
Chromosome Location	chr4:3375722-3375723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10026577	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10212869	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500527	0.83[ASN][1000 genomes]
rs13115912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138393	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844212	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2343800	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28600049	0.80[ASN][1000 genomes]
rs35494582	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58982717	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59594429	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6826720	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843312	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6852922	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs71597208	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7668784	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs7695631	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6855619	CCDC96	cis	parietal	SCAN
rs6855619	GRK4	cis	parietal	SCAN
rs6855619	EXOSC10	trans	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3368800-3376800	Enhancers	Spleen	Spleen
2	chr4:3371200-3375800	Weak transcription	Gastric	stomach
3	chr4:3371600-3378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:3371800-3376000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:3372200-3377400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:3372200-3377600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:3372200-3378000	Weak transcription	Aorta	Aorta
8	chr4:3372200-3382000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:3372400-3377400	Weak transcription	Osteobl	bone
11	chr4:3372400-3377800	Weak transcription	NHDF-Ad	bronchial
12	chr4:3372400-3382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:3372600-3377400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:3372600-3377600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:3373000-3376200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:3373000-3378000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
18	chr4:3373400-3375800	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:3373400-3377400	Weak transcription	HepG2	liver
20	chr4:3373400-3377600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:3373400-3377600	Weak transcription	HSMMtube	muscle
22	chr4:3373400-3380800	Weak transcription	Brain Angular Gyrus	brain
23	chr4:3373400-3382000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
25	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:3373600-3377600	Weak transcription	Fetal Intestine Large	intestine
27	chr4:3373600-3378200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:3373800-3376800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:3373800-3377600	Weak transcription	HSMM	muscle
30	chr4:3373800-3378600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:3374000-3375800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:3374000-3376000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:3374000-3376200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:3374000-3377400	Weak transcription	HUVEC	blood vessel
35	chr4:3374000-3377600	Weak transcription	Primary T cells from cord blood	blood
36	chr4:3374000-3378200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:3374200-3377200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:3374400-3376200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:3374400-3376200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:3374400-3376200	Enhancers	Brain Hippocampus Middle	brain
41	chr4:3374400-3376400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:3374400-3377600	Weak transcription	Fetal Heart	heart
43	chr4:3374400-3377800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:3374400-3379800	Weak transcription	Fetal Lung	lung
45	chr4:3374400-3380800	Weak transcription	Fetal Brain Male	brain
46	chr4:3374600-3376000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:3374600-3378400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr4:3374600-3379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:3374600-3380000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:3374800-3375800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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