Variant report

Variant	rs6426548
Chromosome Location	chr1:227013878-227013879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226827872..226829435-chr1:227013407..227016393,2	MCF-7	breast:
2	chr1:226889929..226892747-chr1:227013300..227016016,3	MCF-7	breast:
3	chr1:226834406..226836488-chr1:227013877..227016506,3	K562	blood:
4	chr1:227006518..227010110-chr1:227013321..227015905,5	K562	blood:
5	chr1:226834406..226836185-chr1:227013877..227015402,2	K562	blood:
6	chr1:227005486..227010136-chr1:227013017..227015365,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1046240	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150897	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11802358	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12086302	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1289396	0.83[AMR][1000 genomes]
rs1295638	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295640	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1295641	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295643	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295647	0.83[ASN][1000 genomes]
rs1296171	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2073489	0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2236914	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236915	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246221	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs2793461	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2802268	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2855559	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855560	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855564	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426541	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6426547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688068	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692729	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514364	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530245	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530370	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8383	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6426548	ARF1	cis	cerebellum	SCAN
rs6426548	PSEN2	cis	parietal	SCAN
rs6426548	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs6426548	ZNF74	trans	parietal	SCAN
rs6426548	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227003400-227015000	Weak transcription	Thymus	Thymus
2	chr1:227009400-227015200	Weak transcription	NHEK	skin
3	chr1:227009600-227014800	Weak transcription	Fetal Kidney	kidney
4	chr1:227009800-227014600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:227009800-227015200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:227009800-227015200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:227009800-227015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:227009800-227015600	Weak transcription	Osteobl	bone
9	chr1:227010000-227014600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:227010000-227014600	Weak transcription	Colonic Mucosa	Colon
11	chr1:227010000-227014800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:227010000-227015000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:227010000-227015200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:227010000-227015200	Weak transcription	Esophagus	oesophagus
15	chr1:227010000-227015200	Weak transcription	Right Ventricle	heart
16	chr1:227010000-227015200	Weak transcription	HSMM	muscle
17	chr1:227010000-227015200	Weak transcription	HUVEC	blood vessel
18	chr1:227010000-227015600	Weak transcription	Left Ventricle	heart
19	chr1:227010200-227014800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:227010200-227014800	Weak transcription	NHDF-Ad	bronchial
21	chr1:227010200-227015200	Weak transcription	Fetal Lung	lung
22	chr1:227010200-227015200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:227010200-227015200	Weak transcription	Right Atrium	heart
24	chr1:227010600-227014800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:227011000-227014600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:227011200-227015200	Enhancers	Brain Substantia Nigra	brain
27	chr1:227011400-227015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:227011400-227015400	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:227011400-227016000	Enhancers	Brain Hippocampus Middle	brain
30	chr1:227011600-227014600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:227011600-227015400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:227011600-227015600	Enhancers	Brain Anterior Caudate	brain
33	chr1:227011800-227015000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:227011800-227015200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:227012000-227014600	Weak transcription	Spleen	Spleen
36	chr1:227012600-227015200	Weak transcription	Primary B cells from cord blood	blood
37	chr1:227013000-227015200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:227013000-227015400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:227013200-227014000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:227013200-227015000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:227013200-227016400	Enhancers	Fetal Muscle Trunk	muscle
42	chr1:227013400-227016200	Enhancers	GM12878-XiMat	blood
43	chr1:227013600-227014600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:227013600-227014800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:227013600-227015600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:227013600-227016200	Enhancers	Placenta	Placenta
47	chr1:227013800-227014200	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:227013800-227014600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:227013800-227014600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:227013800-227014600	Weak transcription	Stomach Smooth Muscle	stomach

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