Variant report

Variant	rs2305957
Chromosome Location	chr4:128732926-128732927
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	chr4:128732822..128735111-chr4:128886290..128887908,2	K562	blood:

Variant related genes	Relation type
ENSG00000164074	Chromatin interaction
ENSG00000164073	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10024450	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10493147	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10857126	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098936	0.84[CEU][hapmap]
rs11098937	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs11098940	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1159021	0.80[GIH][hapmap]
rs11725843	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11735635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12503257	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12504266	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12504825	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12511932	0.84[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs12645636	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs13122568	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs13126673	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs1380154	0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1380156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1459048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1459049	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs1459050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1514299	0.83[CHB][hapmap]
rs1585312	0.84[CEU][hapmap]
rs17012739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870422	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1903104	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs2085655	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2125573	0.83[CHB][hapmap]
rs2305958	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs3214038	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3775982	0.82[CEU][hapmap]
rs3811740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811741	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs3816588	0.86[CEU][hapmap]
rs4435753	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs4543128	0.80[GIH][hapmap]
rs4833383	0.83[CHB][hapmap]
rs4833391	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4834210	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs4834214	0.86[GIH][hapmap]
rs4834217	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs55798529	0.82[EUR][1000 genomes]
rs6534638	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6534647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6534648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6534656	0.81[EUR][1000 genomes]
rs6839292	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs6846535	0.81[EUR][1000 genomes]
rs6847056	0.83[CHB][hapmap]
rs748630	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7654638	0.84[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs7671590	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7684368	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7692114	0.83[CHB][hapmap]
rs7692740	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs769293	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs959822	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9968459	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9995738	0.84[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879921	chr4:128554404-128766074	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
5	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers 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	44 gene(s)	inside rSNPs	diseases
10	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1792152	chr4:128585215-128752829	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv830057	chr4:128591288-128788777	Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv879926	chr4:128652227-128766074	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv879927	chr4:128668850-128766074	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv879928	chr4:128716083-128761940	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2305957	C4orf29	cis	parietal	SCAN
rs2305957	HSPA4L	cis	cerebellum	SCAN
rs2305957	LARP1B	cis	parietal	SCAN
rs2305957	PLK4	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128706000-128743600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:128706200-128759800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:128706400-128741600	Weak transcription	K562	blood
4	chr4:128712000-128764600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:128714400-128760400	Weak transcription	HUVEC	blood vessel
6	chr4:128717400-128744600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:128718000-128760600	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:128719400-128733200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:128719400-128744600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:128719400-128755600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:128722600-128764600	Weak transcription	Esophagus	oesophagus
12	chr4:128725000-128733200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:128727000-128744600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:128727000-128759800	Weak transcription	Brain Angular Gyrus	brain
15	chr4:128728000-128749200	Weak transcription	Brain Substantia Nigra	brain
16	chr4:128729200-128737800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:128729200-128761400	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:128729600-128743600	Weak transcription	Hela-S3	cervix
19	chr4:128729600-128753800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:128730800-128745000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:128730800-128754800	Weak transcription	Liver	Liver
22	chr4:128730800-128755400	Weak transcription	NHEK	skin
23	chr4:128730800-128767000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:128730800-128767200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:128731000-128741000	Weak transcription	HMEC	breast
26	chr4:128732000-128753800	Weak transcription	HepG2	liver
27	chr4:128732000-128761600	Weak transcription	Pancreas	Pancrea
28	chr4:128732000-128764600	Weak transcription	Aorta	Aorta
29	chr4:128732200-128758400	Weak transcription	Left Ventricle	heart
30	chr4:128732600-128733200	Strong transcription	GM12878-XiMat	blood
31	chr4:128732600-128749000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:128732800-128739600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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