Variant report

Variant	rs11650658
Chromosome Location	chr17:67313217-67313218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:67307415..67308999-chr17:67312227..67313741,2	MCF-7	breast:
2	chr17:67312349..67314720-chr17:67316616..67318624,2	MCF-7	breast:
3	chr17:67302738..67306142-chr17:67312679..67315678,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCA10-4	chr17:67313041-67313373	NONHSAT055577

Variant related genes	Relation type
ENSG00000154265	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1011549	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10445224	0.87[ASN][1000 genomes]
rs10512526	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512527	0.85[ASN][1000 genomes]
rs11077445	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11649744	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11650955	0.81[ASN][1000 genomes]
rs11651815	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11651872	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11652207	0.97[ASN][1000 genomes]
rs11654323	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11656389	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11656456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11869324	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12449649	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12450167	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12450522	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12450743	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12452340	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12937191	0.81[AMR][1000 genomes]
rs12937947	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12938064	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12938097	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12940364	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12941297	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12942867	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12943504	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12944980	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12945481	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12946566	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12946776	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949267	0.85[ASN][1000 genomes]
rs12952942	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550828	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1558168	0.83[ASN][1000 genomes]
rs15886	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2364996	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34334829	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34609440	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34985085	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4310935	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310936	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476677	0.86[ASN][1000 genomes]
rs488714	0.87[ASN][1000 genomes]
rs494946	0.86[ASN][1000 genomes]
rs557491	0.87[ASN][1000 genomes]
rs55773491	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57949169	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7213377	0.85[ASN][1000 genomes]
rs7225762	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9646388	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv908706	chr17:67290840-67332355	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
9	nsv575937	chr17:67304447-67327806	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
2	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:67285000-67316200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:67290000-67317400	Weak transcription	Gastric	stomach
5	chr17:67290200-67319600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:67291800-67313800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr17:67291800-67321800	Weak transcription	Esophagus	oesophagus
8	chr17:67293200-67315600	Weak transcription	GM12878-XiMat	blood
9	chr17:67297000-67319400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:67297000-67321800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr17:67304200-67321800	Weak transcription	HUVEC	blood vessel
12	chr17:67305200-67321600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:67306000-67321800	Weak transcription	Placenta	Placenta
14	chr17:67306400-67321000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:67306600-67319600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:67307000-67321800	Weak transcription	Left Ventricle	heart
17	chr17:67307000-67321800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:67307200-67313600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:67307200-67318800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:67307200-67319000	Weak transcription	Fetal Intestine Large	intestine
21	chr17:67307200-67321800	Weak transcription	Thymus	Thymus
22	chr17:67307600-67316000	Weak transcription	NHDF-Ad	bronchial
23	chr17:67308000-67321200	Weak transcription	Fetal Intestine Small	intestine
24	chr17:67310200-67321000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr17:67310800-67316200	Weak transcription	Osteobl	bone
26	chr17:67311000-67315200	Weak transcription	Liver	Liver
27	chr17:67311000-67315600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:67311000-67315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:67311000-67316400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:67311000-67322000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:67311200-67315800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr17:67311200-67319000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:67311200-67319400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr17:67311200-67320400	Weak transcription	Pancreas	Pancrea
35	chr17:67311200-67320400	Weak transcription	Psoas Muscle	Psoas
36	chr17:67311200-67321800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr17:67311200-67322000	Weak transcription	Brain Anterior Caudate	brain
38	chr17:67311400-67315000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr17:67311400-67316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:67311400-67319200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:67311600-67313800	Weak transcription	Brain Substantia Nigra	brain
42	chr17:67312800-67313800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:67312800-67314200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:67313000-67313400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:67313000-67313400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:67313000-67313400	Flanking Active TSS	NHEK	skin
47	chr17:67313200-67314000	Enhancers	HMEC	breast

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