Variant report

Variant	rs3818089
Chromosome Location	chr6:144178419-144178420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144176754..144179141-chr6:144180474..144183385,3	K562	blood:
2	chr6:144178412..144181034-chr6:144184513..144187183,2	K562	blood:
3	chr6:144163789..144165418-chr6:144177348..144179119,2	MCF-7	breast:
4	chr6:144162737..144166210-chr6:144175633..144179990,5	K562	blood:
5	chr6:144163914..144166210-chr6:144177303..144180318,3	K562	blood:

Variant related genes	Relation type
ENSG00000135521	Chromatin interaction
ENSG00000118491	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10872563	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155328	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810524	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884089	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277078	0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2328508	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140442	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4379307	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896676	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4896678	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4896680	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62427458	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918125	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6941262	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773870	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs9484817	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9496785	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144165600-144186800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:144166000-144180200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:144166000-144186000	Strong transcription	Primary B cells from peripheral blood	blood
4	chr6:144166000-144187000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr6:144166000-144188600	Strong transcription	Primary T cells from cord blood	blood
6	chr6:144171200-144182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:144172400-144189000	Weak transcription	Small Intestine	intestine
8	chr6:144172600-144187800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:144172800-144178600	Weak transcription	NHEK	skin
10	chr6:144173000-144178800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:144173000-144179000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:144173800-144186600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:144174800-144184800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:144174800-144187600	Strong transcription	Fetal Thymus	thymus
15	chr6:144175200-144187800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:144175400-144186800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:144175600-144180800	Strong transcription	Brain Anterior Caudate	brain
18	chr6:144175600-144180800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr6:144175600-144185800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:144175600-144186200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:144175600-144186800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:144175600-144187000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:144175600-144187400	Strong transcription	Liver	Liver
24	chr6:144175600-144187400	Strong transcription	Fetal Intestine Large	intestine
25	chr6:144175600-144187600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:144175800-144180600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:144175800-144184800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:144175800-144186000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr6:144175800-144186400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:144175800-144186600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr6:144175800-144186800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr6:144175800-144187000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:144175800-144187600	Strong transcription	Adipose Nuclei	Adipose
34	chr6:144175800-144187600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:144175800-144187800	Strong transcription	Brain Hippocampus Middle	brain
36	chr6:144176000-144187000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:144176200-144179800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:144176200-144181400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:144176200-144185800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:144176200-144186200	Strong transcription	Primary B cells from cord blood	blood
41	chr6:144176200-144186600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:144176200-144186800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:144176200-144186800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:144176200-144187800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:144176400-144178800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:144176400-144180000	Strong transcription	Thymus	Thymus
47	chr6:144176400-144181400	Strong transcription	Brain Angular Gyrus	brain
48	chr6:144176400-144186000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:144176400-144186000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:144176400-144186600	Strong transcription	Osteobl	bone

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