Variant report

Variant	rs504985
Chromosome Location	chr6:149658978-149658979
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149649733..149652455-chr6:149658613..149661110,2	K562	blood:
2	chr6:149638680..149640382-chr6:149658017..149659525,2	MCF-7	breast:
3	chr6:149658537..149661655-chr6:149675884..149678661,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 64 )
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];0.85[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];0.92[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.85[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	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895788	0.80[EUR][1000 genomes];0.85[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]
rs506268	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511100	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs514839	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]
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];0.97[EUR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544947	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580011	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585022	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs600739	0.81[JPT][hapmap]
rs628488	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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];0.82[EUR][1000 genomes];0.86[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];0.82[EUR][1000 genomes];0.86[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];0.88[EUR][1000 genomes];1.00[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373592	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9377212	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs504985	LRP11	cis	cerebellum	SCAN
rs504985	LRP11	cis	parietal	SCAN
rs504985	RAET1E	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
2	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:149648400-149660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:149648600-149659200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:149648600-149659600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:149649000-149660200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:149649400-149659000	Enhancers	Primary T cells from cord blood	blood
10	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
11	chr6:149649800-149660200	Weak transcription	Gastric	stomach
12	chr6:149651400-149660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:149651400-149660000	Enhancers	Liver	Liver
14	chr6:149651600-149659200	Enhancers	Dnd41	blood
15	chr6:149652000-149659000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:149652000-149659400	Enhancers	Brain Anterior Caudate	brain
17	chr6:149652400-149659600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:149652600-149659000	Enhancers	Osteobl	bone
19	chr6:149652600-149659400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:149652600-149659400	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:149652600-149659600	Enhancers	NH-A	brain
22	chr6:149652600-149659800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:149652800-149660000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:149653200-149660200	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:149654000-149674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:149654400-149659400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:149654400-149659400	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:149654600-149668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:149655200-149659400	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:149655400-149659400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:149655400-149660200	Enhancers	Stomach Mucosa	stomach
32	chr6:149655600-149659400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:149655600-149659800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:149655800-149659800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:149655800-149659800	Enhancers	Primary B cells from cord blood	blood
36	chr6:149655800-149660200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:149656000-149659600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:149656200-149659000	Enhancers	HUVEC	blood vessel
39	chr6:149656200-149659400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:149656200-149659600	Enhancers	Hela-S3	cervix
41	chr6:149656200-149670800	Weak transcription	Esophagus	oesophagus
42	chr6:149656400-149659600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr6:149656800-149659000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:149656800-149660000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:149656800-149660200	Enhancers	Brain Angular Gyrus	brain
46	chr6:149656800-149661800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr6:149656800-149681400	Weak transcription	Psoas Muscle	Psoas
48	chr6:149656800-149682400	Weak transcription	Lung	lung
49	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
50	chr6:149657000-149660200	Enhancers	Brain Hippocampus Middle	brain

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