Variant report

Variant	rs3768238
Chromosome Location	chr1:85154697-85154698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85153044..85155913-chr1:85168206..85170903,2	K562	blood:
2	chr1:85038587..85040484-chr1:85154316..85157145,3	K562	blood:
3	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
4	chr1:85151664..85154712-chr1:85171325..85174497,4	K562	blood:
5	chr1:85152648..85155097-chr1:85155098..85157489,2	MCF-7	breast:
6	chr1:85150908..85155231-chr1:85184814..85188587,5	K562	blood:

Variant related genes	Relation type
ENSG00000122432	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1093622	0.89[AMR][1000 genomes]
rs1102838	0.89[AMR][1000 genomes]
rs11578078	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12022113	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12095186	0.81[AMR][1000 genomes]
rs12120614	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12123923	0.89[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs12125951	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs12127432	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1340527	0.99[ASN][1000 genomes]
rs1340528	0.99[ASN][1000 genomes]
rs2298076	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2911567	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2911571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2911575	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2911578	0.99[ASN][1000 genomes]
rs2911583	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2911611	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2943672	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2994429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2994437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2994439	0.94[ASN][1000 genomes]
rs2994440	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2994449	0.97[ASN][1000 genomes]
rs2994941	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2994949	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs3096445	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390189	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4551615	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56681543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576722	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6576723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6670415	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670434	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs6687220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7524511	0.85[JPT][hapmap]
rs818525	0.82[ASN][1000 genomes]
rs9661716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9662145	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947283	chr1:85150944-85155058	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85106400-85155400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85108000-85155000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85126400-85154800	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:85126400-85155200	Weak transcription	Left Ventricle	heart
5	chr1:85138000-85154800	Weak transcription	HSMMtube	muscle
6	chr1:85138800-85155000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:85152000-85155000	Active TSS	Brain Angular Gyrus	brain
8	chr1:85152400-85154800	Weak transcription	Aorta	Aorta
9	chr1:85152600-85156800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:85152800-85155200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:85153000-85155000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:85153200-85154800	Enhancers	HepG2	liver
13	chr1:85153200-85155000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:85153200-85155200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr1:85153400-85154800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:85153400-85154800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:85153400-85155000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:85153600-85154800	Flanking Active TSS	Fetal Brain Male	brain
19	chr1:85153600-85155000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:85153600-85155000	Enhancers	Fetal Heart	heart
21	chr1:85153600-85155200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:85153600-85157000	Active TSS	K562	blood
23	chr1:85153600-85157400	Active TSS	Stomach Smooth Muscle	stomach
24	chr1:85153800-85154800	Flanking Active TSS	NHDF-Ad	bronchial
25	chr1:85154000-85154800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:85154000-85155000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:85154000-85155000	Enhancers	HSMM	muscle
28	chr1:85154000-85155200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:85154000-85155600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:85154000-85156800	Active TSS	GM12878-XiMat	blood
31	chr1:85154200-85154800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:85154200-85154800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:85154200-85154800	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:85154200-85154800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:85154200-85154800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:85154200-85154800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:85154200-85154800	Flanking Active TSS	Fetal Lung	lung
38	chr1:85154200-85155000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:85154200-85155000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:85154200-85155200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:85154200-85155200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:85154200-85155400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:85154200-85155400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:85154200-85155400	Flanking Active TSS	Thymus	Thymus
45	chr1:85154200-85155400	Flanking Active TSS	NHEK	skin
46	chr1:85154200-85155600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:85154400-85154800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:85154400-85154800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:85154400-85154800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:85154400-85154800	Weak transcription	Primary T cells fromperipheralblood	blood

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