Variant report

Variant	rs6674701
Chromosome Location	chr1:227007182-227007183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227006518..227010110-chr1:227013321..227015905,5	K562	blood:
2	chr1:227005486..227010136-chr1:227013017..227015365,4	K562	blood:
3	chr1:227001349..227004344-chr1:227005535..227008816,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1046240	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150897	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150900	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[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];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1289396	0.83[AMR][1000 genomes]
rs1295638	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295640	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1295641	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295643	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295647	0.83[ASN][1000 genomes]
rs1296171	0.83[AMR][1000 genomes];0.85[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];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236915	0.81[ASW][hapmap];0.96[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];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246221	0.81[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap]
rs2793461	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2802268	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2855559	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855560	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855564	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653470	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426541	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6426547	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692729	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697001	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514364	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7530245	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530370	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8383	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674701	PSEN2	cis	parietal	SCAN
rs6674701	ARF1	cis	cerebellum	SCAN
rs6674701	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs6674701	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226995800-227009800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:227003200-227008000	Weak transcription	Right Atrium	heart
3	chr1:227003200-227008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:227003400-227007600	Weak transcription	Left Ventricle	heart
5	chr1:227003400-227007800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:227003400-227008000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:227003400-227008200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:227003400-227008200	Weak transcription	Fetal Lung	lung
9	chr1:227003400-227008200	Weak transcription	Spleen	Spleen
10	chr1:227003400-227008400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:227003400-227008400	Weak transcription	Osteobl	bone
12	chr1:227003400-227008600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:227003400-227008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:227003400-227008600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:227003400-227008600	Weak transcription	HSMM	muscle
16	chr1:227003400-227008600	Weak transcription	HSMMtube	muscle
17	chr1:227003400-227008800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:227003400-227009200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:227003400-227009200	Weak transcription	Right Ventricle	heart
20	chr1:227003400-227009400	Weak transcription	Small Intestine	intestine
21	chr1:227003400-227015000	Weak transcription	Thymus	Thymus
22	chr1:227003600-227007400	Weak transcription	Lung	lung
23	chr1:227003600-227008200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:227003600-227008800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:227003600-227008800	Weak transcription	Psoas Muscle	Psoas
26	chr1:227003600-227009200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:227004000-227008200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:227004000-227008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:227004000-227009200	Weak transcription	Esophagus	oesophagus
30	chr1:227004000-227009400	Weak transcription	Fetal Thymus	thymus
31	chr1:227004200-227008600	Weak transcription	Brain Anterior Caudate	brain
32	chr1:227004200-227008600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:227004200-227009000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:227004200-227011400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:227005000-227007200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:227005000-227008200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:227005000-227008600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:227005000-227008600	Weak transcription	HMEC	breast
39	chr1:227005000-227008800	Weak transcription	NHEK	skin
40	chr1:227005000-227009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:227005200-227007200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:227005200-227008000	Weak transcription	NHDF-Ad	bronchial
43	chr1:227005200-227008400	Weak transcription	NHLF	lung
44	chr1:227005200-227008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:227005200-227008600	Weak transcription	NH-A	brain
46	chr1:227005200-227008800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:227005200-227009200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:227006200-227007200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:227006800-227007400	Flanking Active TSS	HUVEC	blood vessel
50	chr1:227006800-227010800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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