Variant report

Variant	rs209175
Chromosome Location	chr6:28805638-28805639
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28804491..28806748-chr6:28829481..28831000,2	MCF-7	breast:
2	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
3	chr6:28710816..28712847-chr6:28804095..28806646,2	K562	blood:
4	chr6:28804827..28805768-chr6:28983940..28985184,5	MCF-7	breast:
5	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
6	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
7	chr6:28803282..28808495-chr6:28830531..28834946,8	K562	blood:
8	chr6:28804571..28808832-chr6:28889803..28892525,4	MCF-7	breast:
9	chr6:28804431..28805980-chr6:28984572..28985541,9	MCF-7	breast:
10	chr6:28693769..28696400-chr6:28804513..28806706,3	K562	blood:
11	chr6:28805165..28806763-chr6:28869531..28871691,2	K562	blood:
12	chr6:28804427..28806431-chr6:28981603..28983162,2	K562	blood:
13	chr6:28804320..28805825-chr6:28984205..28985476,10	K562	blood:
14	chr6:28804076..28806200-chr6:28922392..28924838,2	K562	blood:
15	chr6:28805205..28806782-chr6:28809772..28812614,2	K562	blood:
16	chr6:28737563..28738090-chr6:28805220..28805859,2	MCF-7	breast:
17	chr6:28804483..28808288-chr6:28953262..28955503,3	MCF-7	breast:
18	chr6:28804831..28806391-chr6:28892543..28895335,2	MCF-7	breast:
19	chr6:28802885..28808466-chr6:28831550..28836351,8	MCF-7	breast:
20	chr6:28805285..28809041-chr6:28890242..28892830,8	K562	blood:
21	chr6:28802724..28808694-chr6:28856997..28865691,21	K562	blood:
22	chr12:49525068..49525631-chr6:28805018..28805686,2	HCT-116	colon:
23	chr6:28805364..28808188-chr6:28994082..28995868,2	K562	blood:
24	chr6:28803772..28806116-chr6:28907591..28909225,2	K562	blood:
25	chr6:28805285..28808440-chr6:28888511..28892745,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223677	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000225595	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1002925	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233602	0.83[EUR][1000 genomes]
rs1237485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476016	0.85[EUR][1000 genomes]
rs169683	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1794587	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs184093	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2032500	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071790	0.84[EUR][1000 genomes]
rs209122	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209126	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209128	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209129	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209138	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs209148	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209149	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209152	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209153	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209160	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209161	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209163	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209164	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209169	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209171	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209176	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209179	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209182	0.86[EUR][1000 genomes]
rs209184	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209186	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2157312	0.82[EUR][1000 genomes]
rs2157313	0.84[EUR][1000 genomes]
rs2208536	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754764	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2754767	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765218	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765219	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765229	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130841	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130842	0.85[EUR][1000 genomes]
rs3130886	0.81[EUR][1000 genomes]
rs3130889	0.85[EUR][1000 genomes]
rs3130897	0.85[EUR][1000 genomes]
rs3131070	0.85[EUR][1000 genomes]
rs3131074	0.85[EUR][1000 genomes]
rs3131077	0.84[EUR][1000 genomes]
rs3131102	0.88[EUR][1000 genomes]
rs3131342	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132371	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132386	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3135303	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135315	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3135322	0.81[EUR][1000 genomes]
rs3135323	0.84[EUR][1000 genomes]
rs3135324	0.84[EUR][1000 genomes]
rs3135327	0.81[EUR][1000 genomes]
rs3135328	0.84[EUR][1000 genomes]
rs377392	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs381808	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs386628	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393431	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs526983	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456857	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs763009	0.82[EUR][1000 genomes]
rs9257229	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28804200-28807400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28804800-28807200	Active TSS	Placenta	Placenta
3	chr6:28804800-28807400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:28804800-28808000	Active TSS	A549	lung
5	chr6:28805000-28805800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:28805000-28806800	Bivalent/Poised TSS	HepG2	liver
7	chr6:28805000-28806800	Active TSS	HUVEC	blood vessel
8	chr6:28805000-28807000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:28805000-28807000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr6:28805000-28807000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:28805000-28807000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:28805000-28807000	Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr6:28805000-28807000	Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:28805000-28807000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
15	chr6:28805000-28807000	Active TSS	Brain Substantia Nigra	brain
16	chr6:28805000-28807200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:28805000-28807200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:28805000-28807200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:28805000-28807200	Active TSS	Hela-S3	cervix
20	chr6:28805000-28807400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr6:28805000-28807400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:28805000-28807400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:28805000-28807400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:28805000-28807400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:28805000-28807400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28805000-28807600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:28805000-28807800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:28805000-28808000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr6:28805200-28805800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr6:28805200-28805800	Bivalent/Poised TSS	Fetal Stomach	stomach
31	chr6:28805200-28805800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:28805200-28806000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:28805200-28806000	Enhancers	Dnd41	blood
34	chr6:28805200-28806200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr6:28805200-28806600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:28805200-28806600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:28805200-28806600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
38	chr6:28805200-28806600	Active TSS	Psoas Muscle	Psoas
39	chr6:28805200-28806600	Active TSS	Right Atrium	heart
40	chr6:28805200-28806800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:28805200-28806800	Active TSS	GM12878-XiMat	blood
42	chr6:28805200-28807000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:28805200-28807000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:28805200-28807000	Active TSS	HMEC	breast
45	chr6:28805200-28807200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:28805200-28807200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:28805200-28807200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:28805200-28807200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr6:28805200-28807200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:28805200-28807200	Active TSS	Brain Cingulate Gyrus	brain

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