Variant report

Variant	rs7678973
Chromosome Location	chr4:120511817-120511818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10518336	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1155577	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12648182	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13104219	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13134517	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1480933	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2389873	0.87[EUR][1000 genomes]
rs2389875	0.83[EUR][1000 genomes]
rs2622501	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2622503	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715016	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892869	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36173322	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3775842	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41464847	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834792	0.87[EUR][1000 genomes]
rs55661135	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56173225	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56843000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59516282	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59590064	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6534135	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66887589	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817317	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6843229	0.82[EUR][1000 genomes]
rs72920701	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661498	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7672519	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7681980	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7694483	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7678973	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs7678973	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
2	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:120492200-120513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:120501800-120520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:120502000-120512400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:120502000-120516200	Weak transcription	Fetal Intestine Large	intestine
11	chr4:120502200-120516400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
13	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
14	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
15	chr4:120503000-120517600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:120503200-120516400	Weak transcription	Ovary	ovary
17	chr4:120503200-120517800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120504400-120516400	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:120504400-120520200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:120504600-120519800	Weak transcription	Fetal Intestine Small	intestine
21	chr4:120505000-120519800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:120505200-120518400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:120505400-120514400	Weak transcription	NH-A	brain
24	chr4:120505400-120516600	Weak transcription	Aorta	Aorta
25	chr4:120505600-120519800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:120506000-120514000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:120506000-120514000	Weak transcription	Fetal Lung	lung
28	chr4:120506000-120515400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:120506000-120516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
31	chr4:120507000-120512800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:120507400-120512400	Weak transcription	Osteobl	bone
33	chr4:120509600-120520000	Weak transcription	Psoas Muscle	Psoas
34	chr4:120509800-120512800	Enhancers	Stomach Smooth Muscle	stomach
35	chr4:120510000-120512600	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr4:120510000-120513000	Enhancers	Colon Smooth Muscle	Colon
37	chr4:120510800-120512800	Genic enhancers	NHLF	lung
38	chr4:120511000-120513200	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:120511000-120515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:120511400-120512200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:120511400-120520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:120511600-120519600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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