Variant report

Variant	rs559052
Chromosome Location	chr6:149653792-149653793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149652416..149655199-chr6:149659324..149661368,2	K562	blood:
2	chr6:149643934..149646869-chr6:149651768..149654461,2	K562	blood:
3	chr6:149636994..149642058-chr6:149649092..149655125,9	MCF-7	breast:
4	chr6:149648554..149650974-chr6:149651371..149654134,3	K562	blood:
5	chr6:149646598..149650161-chr6:149650268..149655691,6	MCF-7	breast:
6	chr6:149637223..149641886-chr6:149650956..149658366,12	K562	blood:
7	chr6:149637223..149639527-chr6:149652423..149654557,3	K562	blood:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs17086451	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2143076	0.86[JPT][hapmap]
rs2341783	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2341784	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744427	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744428	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744431	0.80[EUR][1000 genomes]
rs2744433	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2744434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2789487	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2789488	0.86[JPT][hapmap]
rs2789489	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2789490	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789500	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4360154	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs472620	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs472810	0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs478531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs478767	1.00[CEU][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs480526	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480778	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs481769	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897117	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs490529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492956	1.00[CEU][hapmap];0.94[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];0.99[ASN][1000 genomes]
rs494340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501926	1.00[CEU][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs504762	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504985	0.86[JPT][hapmap]
rs506268	0.81[JPT][hapmap]
rs511105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513923	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs514839	0.86[JPT][hapmap]
rs515133	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs521845	0.86[JPT][hapmap]
rs522646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527971	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs532250	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs533026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536203	0.86[JPT][hapmap]
rs537354	0.86[JPT][hapmap]
rs538386	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540538	0.86[JPT][hapmap]
rs554926	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556335	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560051	0.86[JPT][hapmap]
rs562428	0.86[JPT][hapmap]
rs564405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570442	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577001	0.86[JPT][hapmap]
rs579789	0.86[JPT][hapmap]
rs588028	0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60006373	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs600739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630642	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638407	0.86[JPT][hapmap]
rs641068	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652514	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652807	0.86[JPT][hapmap]
rs652921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570965	0.86[JPT][hapmap]
rs663625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs674919	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs681919	0.84[EUR][1000 genomes]
rs909793	0.86[JPT][hapmap]
rs92605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9285519	0.86[JPT][hapmap]
rs9322178	0.86[JPT][hapmap]
rs9373589	0.86[JPT][hapmap]
rs9373591	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9377216	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377217	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9377218	0.91[JPT][hapmap]
rs9390676	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390677	0.86[JPT][hapmap]
rs9399686	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9404032	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404034	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404035	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404037	0.82[EUR][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	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3331437	chr6:149653722-149654006	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv517889	chr6:149653792-149658118	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149640200-149655400	Weak transcription	Esophagus	oesophagus
2	chr6:149640200-149655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:149641200-149657400	Weak transcription	Aorta	Aorta
4	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
5	chr6:149641400-149655600	Weak transcription	Placenta	Placenta
6	chr6:149641600-149656000	Weak transcription	Lung	lung
7	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:149642600-149657200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:149646200-149654400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr6:149646200-149657400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:149647200-149654400	Weak transcription	Ovary	ovary
14	chr6:149647200-149655400	Weak transcription	Pancreas	Pancrea
15	chr6:149648400-149660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:149648600-149654600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:149648600-149655000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:149648600-149655200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:149648600-149656600	Enhancers	Fetal Heart	heart
20	chr6:149648600-149659200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:149648600-149659600	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:149648800-149656000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:149649000-149657200	Weak transcription	Fetal Intestine Large	intestine
24	chr6:149649000-149660200	Weak transcription	Fetal Intestine Small	intestine
25	chr6:149649200-149654200	Weak transcription	Fetal Kidney	kidney
26	chr6:149649200-149654600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:149649200-149657200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:149649400-149659000	Enhancers	Primary T cells from cord blood	blood
29	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
30	chr6:149649600-149654200	Weak transcription	Right Ventricle	heart
31	chr6:149649600-149654600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:149649800-149654200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:149649800-149654200	Weak transcription	Right Atrium	heart
34	chr6:149649800-149655400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:149649800-149655400	Weak transcription	Left Ventricle	heart
36	chr6:149649800-149655600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:149649800-149660200	Weak transcription	Gastric	stomach
38	chr6:149650600-149656000	Weak transcription	Colonic Mucosa	Colon
39	chr6:149650800-149654200	Weak transcription	Psoas Muscle	Psoas
40	chr6:149650800-149654200	Weak transcription	K562	blood
41	chr6:149650800-149655400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:149650800-149655400	Weak transcription	Spleen	Spleen
43	chr6:149650800-149655600	Weak transcription	Fetal Thymus	thymus
44	chr6:149650800-149655600	Weak transcription	Thymus	Thymus
45	chr6:149650800-149657400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:149651000-149654600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:149651400-149660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:149651400-149660000	Enhancers	Liver	Liver
49	chr6:149651600-149654200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:149651600-149655000	Weak transcription	Placenta Amnion	Placenta Amnion

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