Variant report

Variant	rs35517171
Chromosome Location	chr6:53599975-53599976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53514929..53516623-chr6:53599837..53602771,2	MCF-7	breast:
2	chr6:53516373..53518187-chr6:53597538..53600553,4	MCF-7	breast:
3	chr6:53411604..53413462-chr6:53597893..53600161,2	MCF-7	breast:
4	chr6:53595711..53597938-chr6:53598268..53600839,2	MCF-7	breast:
5	chr6:53583394..53584065-chr6:53599288..53600218,2	MCF-7	breast:
6	chr6:53590810..53593190-chr6:53597036..53600341,4	K562	blood:
7	chr6:53598898..53601641-chr6:53603723..53606379,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10948779	0.89[EUR][1000 genomes]
rs11755346	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000996	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3000997	0.89[EUR][1000 genomes]
rs3000999	0.88[EUR][1000 genomes]
rs3001000	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3001001	0.88[EUR][1000 genomes]
rs3001002	0.86[EUR][1000 genomes]
rs3001009	0.85[EUR][1000 genomes]
rs3001010	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003489	0.85[EUR][1000 genomes]
rs3003491	0.85[EUR][1000 genomes]
rs3003493	0.85[EUR][1000 genomes]
rs3003500	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003501	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34165049	0.94[EUR][1000 genomes]
rs34861916	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880762	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389351	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756855	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813849	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236113	0.85[EUR][1000 genomes]
rs4265033	0.86[EUR][1000 genomes]
rs4276502	0.88[EUR][1000 genomes]
rs4286781	0.85[EUR][1000 genomes]
rs4321822	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4326237	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4336450	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4351263	0.83[EUR][1000 genomes]
rs4382260	0.85[EUR][1000 genomes]
rs4398733	0.85[EUR][1000 genomes]
rs4437471	0.84[EUR][1000 genomes]
rs4484515	0.85[EUR][1000 genomes]
rs4489155	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591854	0.85[EUR][1000 genomes]
rs4615391	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4712048	0.85[EUR][1000 genomes]
rs4712049	0.85[EUR][1000 genomes]
rs4715424	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715426	0.85[EUR][1000 genomes]
rs59641455	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60035355	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458957	0.89[EUR][1000 genomes]
rs6458958	0.86[EUR][1000 genomes]
rs6458959	0.86[EUR][1000 genomes]
rs6458961	0.84[EUR][1000 genomes]
rs6458962	0.84[EUR][1000 genomes]
rs6458965	0.85[EUR][1000 genomes]
rs6458966	0.85[EUR][1000 genomes]
rs6458969	0.85[EUR][1000 genomes]
rs6650996	0.84[EUR][1000 genomes]
rs6899752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920743	0.86[EUR][1000 genomes]
rs6924025	0.85[EUR][1000 genomes]
rs6925836	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926478	0.85[EUR][1000 genomes]
rs6937901	0.85[EUR][1000 genomes]
rs71555560	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739965	0.85[EUR][1000 genomes]
rs7753504	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7754791	0.85[EUR][1000 genomes]
rs7759946	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762883	0.84[EUR][1000 genomes]
rs7763081	0.85[EUR][1000 genomes]
rs7763147	0.86[EUR][1000 genomes]
rs7769893	0.89[EUR][1000 genomes]
rs9296719	0.85[EUR][1000 genomes]
rs9296721	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9367544	0.82[EUR][1000 genomes]
rs9370235	0.85[EUR][1000 genomes]
rs9370239	0.83[EUR][1000 genomes]
rs9382234	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382237	0.89[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:53596000-53601600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:53597400-53600000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:53598400-53601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53598400-53601200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:53598400-53601400	Enhancers	Fetal Intestine Small	intestine
9	chr6:53598400-53603000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:53598600-53601400	Enhancers	Fetal Intestine Large	intestine
11	chr6:53599000-53600000	Enhancers	Stomach Mucosa	stomach
12	chr6:53599000-53600400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:53599000-53601000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:53599200-53600000	Flanking Active TSS	A549	lung
15	chr6:53599200-53600600	Enhancers	HSMM	muscle
16	chr6:53599200-53601200	Enhancers	Duodenum Mucosa	Duodenum
17	chr6:53599200-53603000	Enhancers	Fetal Heart	heart
18	chr6:53599400-53600000	Flanking Active TSS	Hela-S3	cervix
19	chr6:53599400-53600000	Flanking Active TSS	NH-A	brain
20	chr6:53599400-53600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:53599400-53601000	Enhancers	GM12878-XiMat	blood
22	chr6:53599400-53601200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:53599400-53601200	Enhancers	Fetal Thymus	thymus
24	chr6:53599400-53601200	Enhancers	Thymus	Thymus
25	chr6:53599400-53602200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:53599400-53602600	Enhancers	HSMMtube	muscle
27	chr6:53599600-53600000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr6:53599600-53600000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53599600-53600000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:53599600-53600000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:53599600-53600000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr6:53599600-53600000	Flanking Active TSS	HMEC	breast
33	chr6:53599600-53600200	Enhancers	Left Ventricle	heart
34	chr6:53599600-53600800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:53599600-53600800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr6:53599600-53601000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:53599600-53601000	Enhancers	Placenta	Placenta
38	chr6:53599600-53601200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:53599600-53601200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr6:53599600-53601200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:53599800-53600000	Enhancers	Esophagus	oesophagus
42	chr6:53599800-53600000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:53599800-53600000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr6:53599800-53600800	Flanking Active TSS	Dnd41	blood
45	chr6:53599800-53601000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:53599800-53601000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:53599800-53601000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr6:53599800-53601000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:53599800-53601000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:53599800-53601000	Enhancers	Monocytes-CD14+_RO01746	blood

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