Variant report

Variant	rs6857442
Chromosome Location	chr4:15653353-15653354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15652688..15657004-chr4:15659488..15663550,8	K562	blood:
2	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
3	chr4:15651951..15654188-chr4:15659620..15662479,2	K562	blood:
4	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
5	chr4:15652202..15654659-chr4:15668639..15670937,2	MCF-7	breast:
6	chr4:15479691..15482462-chr4:15651754..15655275,3	MCF-7	breast:
7	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction
ENSG00000237765	Chromatin interaction
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10005305	0.91[AFR][1000 genomes]
rs10008878	0.93[AFR][1000 genomes]
rs10009089	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015827	0.81[ASN][1000 genomes]
rs10017222	0.81[ASN][1000 genomes]
rs10025875	0.94[AFR][1000 genomes]
rs10034315	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433813	0.81[ASN][1000 genomes]
rs11722757	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726647	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732953	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12642407	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650529	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134177	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13150957	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28394730	0.95[AFR][1000 genomes]
rs28402170	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28447067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28820655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34473224	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34559117	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34955342	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35013326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120298	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756247	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3775956	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3775957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257653	0.96[ASN][1000 genomes]
rs4301111	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331772	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346644	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396986	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4423870	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549375	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4554069	0.95[AFR][1000 genomes]
rs4600905	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698116	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449152	0.81[ASN][1000 genomes]
rs6815254	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6816982	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823775	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824422	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825051	0.80[AFR][1000 genomes]
rs6826058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827406	0.81[ASN][1000 genomes]
rs6828776	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839654	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6843740	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6848779	0.93[AFR][1000 genomes]
rs6852735	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667175	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7698596	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9994518	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3464809	chr4:15646178-15656952	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv3464811	chr4:15646243-15656896	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv3464810	chr4:15646249-15656868	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv3464812	chr4:15646332-15656829	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15568400-15655600	Weak transcription	Gastric	stomach
2	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
3	chr4:15622200-15655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:15628000-15655600	Weak transcription	Lung	lung
5	chr4:15635600-15655600	Weak transcription	Esophagus	oesophagus
6	chr4:15635800-15654800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:15638800-15655000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:15641800-15653600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:15642000-15655200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:15642000-15656200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:15643600-15653400	Weak transcription	Thymus	Thymus
12	chr4:15643600-15653600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:15643600-15654800	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:15643600-15655600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:15644600-15653400	Weak transcription	Fetal Kidney	kidney
16	chr4:15647200-15655000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:15647400-15653400	Weak transcription	Psoas Muscle	Psoas
18	chr4:15647600-15655000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr4:15649000-15653600	Enhancers	Primary T cells from cord blood	blood
20	chr4:15649000-15655000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr4:15649200-15654400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:15649200-15654600	Enhancers	Colon Smooth Muscle	Colon
23	chr4:15649200-15655000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:15649200-15655000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr4:15649200-15655200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:15649400-15655000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:15649600-15654600	Enhancers	Brain Hippocampus Middle	brain
28	chr4:15649600-15654800	Enhancers	Adipose Nuclei	Adipose
29	chr4:15649600-15654800	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:15650000-15653600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:15650000-15655200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:15650200-15653400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:15650200-15655000	Enhancers	Brain Cingulate Gyrus	brain
34	chr4:15650800-15654000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:15650800-15654400	Enhancers	Fetal Lung	lung
36	chr4:15650800-15655000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:15651000-15655000	Weak transcription	Right Ventricle	heart
38	chr4:15651200-15653400	Enhancers	Primary hematopoietic stem cells	blood
39	chr4:15651200-15653400	Weak transcription	Left Ventricle	heart
40	chr4:15651200-15653400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:15651400-15653400	Enhancers	Primary B cells from cord blood	blood
42	chr4:15651400-15653800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:15651400-15653800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr4:15651400-15654400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr4:15651400-15654400	Enhancers	HepG2	liver
46	chr4:15651400-15654800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr4:15651400-15655000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:15651400-15655000	Enhancers	Fetal Heart	heart
49	chr4:15651400-15655000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:15651600-15653400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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