Variant report

Variant	rs17715106
Chromosome Location	chr3:46422645-46422646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46414355..46417313-chr3:46422093..46423831,2	K562	blood:
2	chr3:46420928..46423796-chr3:46462092..46464094,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs11574430	0.90[ASN][1000 genomes]
rs11574436	0.90[ASN][1000 genomes]
rs11574442	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575062	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13065351	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13068145	0.86[ASN][1000 genomes]
rs13068271	0.86[ASN][1000 genomes]
rs13071469	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13073976	1.00[AFR][1000 genomes]
rs13077302	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13078564	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13080757	1.00[AFR][1000 genomes]
rs13093063	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13100243	0.86[ASN][1000 genomes]
rs17141079	1.00[ASN][1000 genomes]
rs17141101	0.90[ASN][1000 genomes]
rs17283712	1.00[AFR][1000 genomes]
rs17284138	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17284187	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17285143	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17765882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782551	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782618	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782636	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894387	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1894388	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2097285	0.94[EUR][1000 genomes]
rs2157053	1.00[AFR][1000 genomes]
rs2157055	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2373245	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2373250	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2373251	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2856762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677778	0.86[ASN][1000 genomes]
rs3091310	1.00[AFR][1000 genomes]
rs3092957	1.00[ASN][1000 genomes]
rs3092958	1.00[ASN][1000 genomes]
rs3092959	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3181038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204850	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34024447	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34041956	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34073838	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34079287	1.00[AFR][1000 genomes]
rs34106161	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34158148	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34180919	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34190223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34200951	0.95[ASN][1000 genomes]
rs34203322	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34245951	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34265215	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34351442	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34363105	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34448949	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34455547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473395	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34578126	0.95[ASN][1000 genomes]
rs34671664	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34709208	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34883716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953706	1.00[ASN][1000 genomes]
rs34988015	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34997818	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35117954	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35118578	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35148665	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35203745	0.86[ASN][1000 genomes]
rs35218998	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35260614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35367413	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35373513	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35386789	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35413141	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35438577	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35479331	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35511592	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35513549	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35516519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35568430	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35577626	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35601704	1.00[ASN][1000 genomes]
rs35646896	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35821444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35878193	0.95[ASN][1000 genomes]
rs35883833	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35943069	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36020695	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36030692	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36052732	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36078103	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3749461	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3918354	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3918362	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3918365	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3918368	0.83[ASN][1000 genomes]
rs4473594	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6777875	1.00[ASN][1000 genomes]
rs6793370	0.86[ASN][1000 genomes]
rs6806951	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71327048	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs71327052	1.00[ASN][1000 genomes]
rs71327053	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71327054	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71327055	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71327056	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71327057	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71327059	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327061	1.00[ASN][1000 genomes]
rs71327062	0.95[ASN][1000 genomes]
rs71327063	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71615445	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7649905	0.86[ASN][1000 genomes]
rs9714000	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9810242	0.86[ASN][1000 genomes]
rs9882616	0.86[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756988	chr3:46419634-46444794	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2759146	chr3:46419634-46444794	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
2	chr3:46420000-46423000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:46420400-46425400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:46420400-46427600	Weak transcription	Pancreas	Pancrea
5	chr3:46421000-46423000	Enhancers	Primary B cells from cord blood	blood
6	chr3:46421400-46422800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:46421400-46422800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:46421400-46422800	Enhancers	Fetal Thymus	thymus
9	chr3:46421400-46423000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:46421400-46423400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:46421400-46426000	Enhancers	Fetal Lung	lung
12	chr3:46421600-46423000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:46421600-46423000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:46421600-46423000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:46421600-46423000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:46421600-46423000	Enhancers	Brain Anterior Caudate	brain
20	chr3:46421600-46424000	Enhancers	Fetal Brain Male	brain
21	chr3:46421800-46423000	Enhancers	Primary T cells from cord blood	blood
22	chr3:46421800-46423000	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:46421800-46425000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:46422000-46422800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:46422000-46422800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:46422000-46422800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:46422000-46422800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:46422000-46422800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr3:46422000-46422800	Enhancers	HMEC	breast
30	chr3:46422000-46423000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:46422000-46423000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:46422000-46423000	Enhancers	Liver	Liver
33	chr3:46422000-46423000	Enhancers	Brain Hippocampus Middle	brain
34	chr3:46422000-46423000	Enhancers	Colon Smooth Muscle	Colon
35	chr3:46422000-46423000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:46422000-46423000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr3:46422000-46423400	Enhancers	Small Intestine	intestine
38	chr3:46422000-46423600	Enhancers	Adipose Nuclei	Adipose
39	chr3:46422000-46423800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:46422000-46424000	Enhancers	Ovary	ovary
41	chr3:46422000-46425200	Enhancers	Colonic Mucosa	Colon
42	chr3:46422200-46422800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:46422200-46422800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr3:46422200-46423000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:46422200-46423000	Enhancers	HSMM	muscle
46	chr3:46422200-46425400	Enhancers	Stomach Mucosa	stomach
47	chr3:46422200-46435200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:46422400-46423200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:46422400-46423200	Weak transcription	Fetal Brain Female	brain
50	chr3:46422400-46423200	Weak transcription	Gastric	stomach

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