Variant report

Variant	rs9475716
Chromosome Location	chr6:56402958-56402959
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56398077..56400962-chr6:56401619..56403800,2	K562	blood:
2	chr6:56396433..56398982-chr6:56400861..56403143,2	MCF-7	breast:
3	chr6:56393226..56394746-chr6:56401973..56403869,2	MCF-7	breast:
4	chr6:56402144..56405169-chr6:56405351..56407605,3	MCF-7	breast:
5	chr6:56402109..56404865-chr6:56433971..56436313,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11759493	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11961668	0.81[EUR][1000 genomes]
rs12527139	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204556	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13219448	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1359068	0.81[EUR][1000 genomes]
rs1359070	0.81[EUR][1000 genomes]
rs1535612	0.81[ASN][1000 genomes]
rs16887974	0.91[ASN][1000 genomes]
rs2273974	0.82[EUR][1000 genomes]
rs2397226	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34954984	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35671304	0.81[EUR][1000 genomes]
rs35926142	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130060	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4143827	0.82[EUR][1000 genomes]
rs4143828	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4236140	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236141	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236142	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4236143	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4236144	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4236145	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4283892	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4329120	0.82[EUR][1000 genomes]
rs4331988	0.82[EUR][1000 genomes]
rs4346846	0.82[EUR][1000 genomes]
rs4454141	0.82[EUR][1000 genomes]
rs4466244	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4473850	0.84[EUR][1000 genomes]
rs4499917	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544910	0.81[EUR][1000 genomes]
rs45486696	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4712132	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4712133	0.91[ASN][1000 genomes]
rs4715625	0.81[EUR][1000 genomes]
rs4715626	0.82[EUR][1000 genomes]
rs4715627	0.82[EUR][1000 genomes]
rs4715628	0.82[EUR][1000 genomes]
rs4715630	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459163	0.81[EUR][1000 genomes]
rs6906792	0.83[EUR][1000 genomes]
rs6907917	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6913572	0.82[EUR][1000 genomes]
rs6922770	0.80[EUR][1000 genomes]
rs6939305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72877350	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7741295	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743011	0.82[EUR][1000 genomes]
rs7746753	0.81[EUR][1000 genomes]
rs7755361	0.82[EUR][1000 genomes]
rs7755573	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7758054	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760695	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761281	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7762629	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296848	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296849	0.82[EUR][1000 genomes]
rs9296850	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349826	0.82[EUR][1000 genomes]
rs9357921	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357922	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370535	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396214	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396215	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9464389	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475709	0.81[ASN][1000 genomes]
rs9475713	0.82[EUR][1000 genomes]
rs9475714	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56376400-56407200	Weak transcription	Gastric	stomach
3	chr6:56377200-56404200	Weak transcription	K562	blood
4	chr6:56390600-56403800	Weak transcription	Thymus	Thymus
5	chr6:56390800-56403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:56392400-56406200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:56395400-56405200	Weak transcription	Placenta	Placenta
8	chr6:56397000-56403600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:56397000-56405200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:56397200-56406600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:56397400-56405600	Weak transcription	Fetal Brain Female	brain
12	chr6:56398200-56405000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:56399600-56403000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:56399800-56403000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:56400000-56404200	Weak transcription	Stomach Mucosa	stomach
16	chr6:56400000-56404600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:56400000-56405400	Weak transcription	Fetal Thymus	thymus
18	chr6:56400200-56403000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:56400200-56404200	Weak transcription	A549	lung
20	chr6:56400200-56404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:56400200-56405200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:56400200-56405800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:56400400-56407000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:56400600-56403000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56400800-56403000	Transcr. at gene 5' and 3'	Fetal Lung	lung
26	chr6:56400800-56403800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:56400800-56404000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:56400800-56404600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:56401000-56404600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:56401200-56403000	Enhancers	Psoas Muscle	Psoas
31	chr6:56401200-56403400	Enhancers	Brain Cingulate Gyrus	brain
32	chr6:56401200-56404200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:56401200-56404200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:56401400-56403000	Enhancers	Pancreas	Pancrea
35	chr6:56401400-56403400	Enhancers	NH-A	brain
36	chr6:56401400-56403600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:56401400-56404400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:56401600-56403000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:56401600-56403000	Strong transcription	HSMMtube	muscle
40	chr6:56401600-56403200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:56401600-56403200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:56401600-56403200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:56401600-56403400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:56401600-56403600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:56401600-56404000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:56401600-56404000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:56401600-56404200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:56401600-56404200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:56401600-56404800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:56401600-56405000	Weak transcription	Colonic Mucosa	Colon

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