Variant report

Variant	rs514839
Chromosome Location	chr6:149648440-149648441
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149535644..149537986-chr6:149647515..149649040,2	K562	blood:
2	chr6:149643394..149646422-chr6:149647403..149650011,4	K562	blood:
3	chr6:149647673..149650092-chr6:149672445..149675357,2	K562	blood:
4	chr6:149644563..149647339-chr6:149647427..149650792,4	K562	blood:
5	chr6:149646598..149650161-chr6:149650268..149655691,6	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs2143076	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744434	0.87[JPT][hapmap]
rs2789488	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.82[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.87[JPT][hapmap]
rs472810	0.85[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.86[JPT][hapmap]
rs489551	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895788	0.82[ASN][1000 genomes]
rs4895789	0.95[CEU][hapmap]
rs492956	0.85[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.82[JPT][hapmap]
rs504985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506268	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511100	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs515133	0.83[JPT][hapmap]
rs521845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532250	0.83[JPT][hapmap]
rs536203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544947	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556335	0.87[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs560051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.82[JPT][hapmap]
rs577001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580011	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585022	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs600739	0.81[JPT][hapmap]
rs628488	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap]
rs6570965	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs909793	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs9285519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373589	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9373592	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377212	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377218	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs9390676	0.86[JPT][hapmap]
rs9390677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs514839	LRP11	cis	parietal	SCAN
rs514839	RAET1E	cis	cerebellum	SCAN
rs514839	LRP11	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149640000-149649400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:149640200-149655400	Weak transcription	Esophagus	oesophagus
3	chr6:149640200-149655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:149640400-149648600	Weak transcription	Right Ventricle	heart
5	chr6:149640600-149648600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:149640800-149649000	Weak transcription	Thymus	Thymus
7	chr6:149640800-149652800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:149640800-149653200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:149641200-149649200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:149641200-149657400	Weak transcription	Aorta	Aorta
11	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
12	chr6:149641400-149655600	Weak transcription	Placenta	Placenta
13	chr6:149641600-149649400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:149641600-149652600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:149641600-149656000	Weak transcription	Lung	lung
16	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:149642000-149648800	Enhancers	Primary T cells from cord blood	blood
19	chr6:149642200-149649200	Weak transcription	K562	blood
20	chr6:149642200-149652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:149642400-149649400	Weak transcription	Psoas Muscle	Psoas
22	chr6:149642400-149650200	Weak transcription	Primary B cells from cord blood	blood
23	chr6:149642400-149652600	Weak transcription	NH-A	brain
24	chr6:149642400-149652600	Weak transcription	NHLF	lung
25	chr6:149642600-149652600	Weak transcription	NHDF-Ad	bronchial
26	chr6:149642600-149657200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:149642800-149650400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:149643000-149653400	Weak transcription	HSMM	muscle
29	chr6:149643400-149652200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:149644800-149648600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:149645000-149648600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:149645200-149649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:149645600-149652600	Weak transcription	Osteobl	bone
35	chr6:149645800-149648600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:149645800-149648600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:149645800-149651800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:149645800-149651800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:149645800-149652800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:149646000-149648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:149646000-149648600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:149646000-149648600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:149646000-149648600	Weak transcription	Small Intestine	intestine
44	chr6:149646000-149649000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:149646000-149649400	Weak transcription	Left Ventricle	heart
46	chr6:149646000-149651400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:149646000-149652600	Weak transcription	HMEC	breast
48	chr6:149646200-149648600	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:149646200-149649000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:149646200-149650400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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