Variant report

Variant	rs1461024
Chromosome Location	chr1:173498017-173498018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173490173..173492783-chr1:173495928..173498517,3	K562	blood:
2	chr1:173496870..173499125-chr1:173501747..173503656,2	K562	blood:
3	chr1:173496493..173499619-chr1:173501510..173504618,3	K562	blood:
4	chr1:173496848..173499075-chr1:173504402..173505965,2	MCF-7	breast:
5	chr1:173490173..173491820-chr1:173495928..173498517,2	K562	blood:
6	chr1:173496692..173499395-chr1:173502096..173503958,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10753082	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753083	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912624	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs10912633	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912643	0.87[YRI][hapmap]
rs10912650	0.84[AMR][1000 genomes]
rs12075314	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080722	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745058	0.80[AFR][1000 genomes]
rs1359460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461014	0.82[YRI][hapmap]
rs1461022	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461025	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547154	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570813	0.82[AMR][1000 genomes]
rs1886638	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382766	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs4405161	1.00[JPT][hapmap]
rs4472784	1.00[JPT][hapmap]
rs4573551	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4916366	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916367	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916371	0.82[AMR][1000 genomes]
rs7314	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs7535963	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540065	0.85[ASW][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap]
rs7551305	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912768	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425411	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1461024	RABGAP1L	cis	lymphoblastoid	seeQTL
rs1461024	TNFSF4	cis	parietal	SCAN
rs1461024	PRDX6	cis	parietal	SCAN
rs1461024	DARS2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173495000-173500200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:173496400-173498400	Weak transcription	K562	blood
3	chr1:173496400-173498800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr1:173496400-173501200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:173496400-173501800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:173496600-173498800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:173496600-173499000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:173496800-173498200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:173496800-173499200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:173496800-173499200	Weak transcription	Placenta	Placenta
11	chr1:173496800-173500400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:173496800-173501200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:173496800-173501600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:173497000-173500400	Weak transcription	Adipose Nuclei	Adipose
15	chr1:173497200-173499400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:173497200-173500400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:173497400-173498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:173497400-173498600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:173497400-173500400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:173497600-173498800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:173497600-173499000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:173497600-173500400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:173497800-173498400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:173497800-173498600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:173497800-173498800	Enhancers	Primary T cells from cord blood	blood
26	chr1:173497800-173499200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:173497800-173499800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:173497800-173500000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:173498000-173498600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:173498000-173498800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:173498000-173499800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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