Variant report

Variant	rs1970559
Chromosome Location	chr1:114377148-114377149
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114352576..114359844-chr1:114370702..114381098,32	MCF-7	breast:
2	chr1:114377132..114380200-chr1:114444607..114447875,4	MCF-7	breast:
3	chr1:114372290..114377468-chr1:114470265..114473601,5	MCF-7	breast:
4	chr1:114376437..114378781-chr1:114506085..114507975,2	MCF-7	breast:
5	chr1:114344419..114346112-chr1:114376286..114378764,3	MCF-7	breast:
6	chr1:114375425..114378067-chr1:114378489..114380651,2	K562	blood:
7	chr1:114371649..114374466-chr1:114376496..114379359,3	K562	blood:
8	chr1:114376626..114379778-chr1:114446255..114449458,6	K562	blood:
9	chr1:114377082..114381758-chr1:114445444..114449368,6	MCF-7	breast:
10	chr1:114366150..114373270-chr1:114373613..114381825,12	MCF-7	breast:
11	chr1:114353356..114357634-chr1:114372814..114380576,14	MCF-7	breast:
12	chr1:114372966..114375682-chr1:114376840..114378466,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10858015	0.81[ASN][1000 genomes]
rs11102678	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1146183	0.82[CHB][hapmap];1.00[CHD][hapmap];0.80[TSI][hapmap]
rs1146184	0.82[CHB][hapmap]
rs1146185	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1217375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217378	0.82[AFR][1000 genomes]
rs1217379	0.93[LWK][hapmap]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.90[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217404	0.80[AFR][1000 genomes]
rs1217405	0.93[AFR][1000 genomes]
rs1217406	0.97[LWK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs1217408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217414	1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217417	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217418	0.97[LWK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs1217419	0.97[LWK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes]
rs1217420	0.84[AFR][1000 genomes]
rs1230673	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs1230681	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1230684	0.91[ASN][1000 genomes]
rs1310182	0.95[AFR][1000 genomes]
rs13524	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs1743594	0.85[CHD][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs1746857	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2040041	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2185827	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476599	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2476600	0.93[LWK][hapmap];0.80[AFR][1000 genomes]
rs2476602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476604	0.93[AFR][1000 genomes]
rs2636000	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2636003	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs2797416	0.93[LWK][hapmap];0.80[AFR][1000 genomes]
rs3789597	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs3789598	0.83[YRI][hapmap]
rs3789600	0.95[LWK][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs4991898	0.85[AFR][1000 genomes]
rs6537798	0.88[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs7555634	0.93[LWK][hapmap]
rs971173	0.90[JPT][hapmap]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
3	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:114356000-114377400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:114357200-114377600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:114357200-114377800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:114358400-114377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:114358600-114377600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:114361800-114390400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:114365400-114377600	Strong transcription	GM12878-XiMat	blood
13	chr1:114366800-114379600	Weak transcription	Primary T cells from cord blood	blood
14	chr1:114369000-114380000	Weak transcription	Thymus	Thymus
15	chr1:114370000-114377600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:114373800-114377400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:114375200-114377600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:114375200-114377600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:114375200-114377600	Strong transcription	Fetal Thymus	thymus
20	chr1:114375600-114377600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:114375800-114377600	Strong transcription	Primary B cells from cord blood	blood
22	chr1:114376200-114377400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:114376200-114377600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:114376200-114377600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:114376200-114377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:114376400-114377400	Strong transcription	Dnd41	blood
27	chr1:114376600-114377400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:114376600-114377600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:114376600-114377600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:114376800-114377600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:114376800-114377600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:114376800-114377600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:114376800-114377600	Enhancers	NHEK	skin
34	chr1:114376800-114378000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:114377000-114377600	Enhancers	HMEC	breast

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