Variant report

Variant	rs6858855
Chromosome Location	chr4:128617730-128617731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1018289	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857125	0.85[EUR][1000 genomes]
rs11098931	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1159021	0.82[CEU][hapmap]
rs11728750	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732886	0.92[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12331481	0.87[EUR][1000 genomes]
rs12509562	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12511932	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12649427	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650360	0.91[ASN][1000 genomes]
rs13126673	0.85[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs13151291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1399211	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459049	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs1459051	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1514298	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1514299	0.81[CEU][hapmap]
rs1913464	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048686	0.87[ASN][1000 genomes]
rs2125573	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2255457	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2391188	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391189	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34066758	0.89[EUR][1000 genomes]
rs34240473	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36179490	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749507	0.81[CEU][hapmap]
rs4543128	0.85[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4833380	0.87[EUR][1000 genomes]
rs4833383	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs4833384	0.87[EUR][1000 genomes]
rs4833386	0.89[EUR][1000 genomes]
rs4834209	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4834210	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4834211	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4834214	0.82[CEU][hapmap]
rs59255549	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62334037	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534631	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6534632	0.81[CEU][hapmap]
rs6534633	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534634	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534637	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810904	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823957	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6828511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847397	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678085	0.85[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs7683627	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7686395	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692114	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7694079	0.87[EUR][1000 genomes]
rs922060	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv879920	chr4:128554404-128694288	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv879924	chr4:128566686-128622430	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	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
16	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
17	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
18	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
19	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
20	nsv879925	chr4:128586241-128665981	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6858855	HSPA4L	cis	cerebellum	SCAN
rs6858855	PGRMC2	cis	parietal	SCAN
rs6858855	LARP1B	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128554600-128627400	Weak transcription	Pancreas	Pancrea
2	chr4:128554600-128644800	Weak transcription	Lung	lung
3	chr4:128555600-128627600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:128563600-128627400	Weak transcription	Brain Substantia Nigra	brain
5	chr4:128566600-128644600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:128597000-128630200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:128597000-128651600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:128597600-128632000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:128597600-128632000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:128597800-128627600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:128598200-128627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:128598200-128638200	Weak transcription	Esophagus	oesophagus
13	chr4:128604400-128634400	Weak transcription	Fetal Heart	heart
14	chr4:128606200-128627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:128606200-128638200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:128607000-128627400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:128607600-128627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:128607800-128627400	Weak transcription	Left Ventricle	heart
19	chr4:128608000-128619600	Weak transcription	NH-A	brain
20	chr4:128608400-128619800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:128608400-128630200	Weak transcription	Gastric	stomach
22	chr4:128608400-128643800	Weak transcription	Right Ventricle	heart
23	chr4:128608800-128619600	Weak transcription	NHEK	skin
24	chr4:128609200-128627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:128609800-128636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:128611200-128627800	Weak transcription	Fetal Stomach	stomach
27	chr4:128612200-128619600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:128612200-128620000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:128612200-128632200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:128612800-128626600	Weak transcription	Adipose Nuclei	Adipose
31	chr4:128614800-128627600	Weak transcription	HSMMtube	muscle
32	chr4:128615200-128642000	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:128615200-128648800	Weak transcription	Fetal Kidney	kidney
34	chr4:128615400-128630200	Weak transcription	Brain Germinal Matrix	brain
35	chr4:128616200-128618200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:128616200-128619400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:128616200-128626600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:128616200-128627800	Weak transcription	Fetal Lung	lung
39	chr4:128616200-128646200	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:128616400-128625400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:128616400-128627400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:128616400-128627400	Weak transcription	Fetal Brain Female	brain
43	chr4:128616400-128627400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:128616600-128627400	Weak transcription	Aorta	Aorta
45	chr4:128616800-128626400	Weak transcription	Ovary	ovary
46	chr4:128617000-128618400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:128617000-128619400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:128617000-128627400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:128617000-128643400	Weak transcription	Fetal Intestine Small	intestine
50	chr4:128617200-128618200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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