Variant report

Variant	rs16859405
Chromosome Location	chr2:172345151-172345152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172344598..172348821-chr2:172376554..172380965,4	K562	blood:
2	chr2:172337093..172339286-chr2:172342901..172345235,2	K562	blood:
3	chr2:172048062..172050725-chr2:172343966..172345491,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCAF17-1	chr2:172345084-172345288	XLOC_001752

Variant related genes	Relation type
ENSG00000071967	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs16859368	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859377	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17287497	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17287624	0.91[ASN][1000 genomes]
rs1882378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731984	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55711751	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55715902	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55716501	1.00[EUR][1000 genomes]
rs55974181	0.96[EUR][1000 genomes]
rs56065525	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56239048	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56273218	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56302833	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57165050	0.92[EUR][1000 genomes]
rs61021737	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61502503	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6759487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs728651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72882347	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72882363	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73021048	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73976175	0.96[EUR][1000 genomes]
rs9646734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart
3	chr2:172327000-172346800	Weak transcription	Colonic Mucosa	Colon
4	chr2:172327200-172346600	Weak transcription	Thymus	Thymus
5	chr2:172327200-172348800	Weak transcription	Spleen	Spleen
6	chr2:172327400-172346800	Weak transcription	Hela-S3	cervix
7	chr2:172327400-172347600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:172327800-172346000	Weak transcription	Fetal Brain Male	brain
9	chr2:172330400-172346200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:172331400-172345800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:172333400-172345400	Weak transcription	NHDF-Ad	bronchial
12	chr2:172333400-172347800	Weak transcription	Brain Angular Gyrus	brain
13	chr2:172334600-172349200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:172334800-172345200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:172334800-172346200	Weak transcription	Psoas Muscle	Psoas
16	chr2:172334800-172346800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:172334800-172347200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:172334800-172349200	Weak transcription	Esophagus	oesophagus
19	chr2:172335200-172346400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:172335400-172349000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:172337800-172348000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:172338000-172345600	Weak transcription	Fetal Thymus	thymus
23	chr2:172338000-172349400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:172338200-172347000	Weak transcription	HMEC	breast
25	chr2:172338400-172349800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:172338600-172345400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:172339600-172345400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:172339600-172347800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:172339600-172348000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:172339800-172348000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:172339800-172350600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:172339800-172352200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:172340000-172345200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:172340000-172345200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:172340000-172345400	Weak transcription	Fetal Intestine Large	intestine
36	chr2:172340000-172347000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:172340000-172347800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:172340000-172348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:172340000-172348000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:172340000-172348000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:172340000-172348600	Weak transcription	Ovary	ovary
42	chr2:172340000-172351200	Weak transcription	Aorta	Aorta
43	chr2:172340000-172368400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:172340400-172348000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:172341000-172348000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:172342000-172345200	Weak transcription	Dnd41	blood
47	chr2:172342200-172347000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:172342200-172348200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:172342200-172348600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:172342800-172345200	Weak transcription	Monocytes-CD14+_RO01746	blood

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