Variant report

Variant	rs2246221
Chromosome Location	chr1:227075402-227075403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227073623..227075968-chr1:227085768..227087607,2	K562	blood:
2	chr1:227072686..227076463-chr1:227077857..227081301,5	K562	blood:
3	chr1:227063913..227065661-chr1:227075217..227077074,2	MCF-7	breast:
4	chr1:227071996..227075968-chr1:227085768..227088327,4	K562	blood:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1046240	0.85[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1150897	0.87[EUR][1000 genomes]
rs1150900	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12086302	0.85[EUR][1000 genomes]
rs1295638	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs1295640	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs1295641	0.90[EUR][1000 genomes]
rs1295643	0.90[EUR][1000 genomes]
rs1296171	0.87[EUR][1000 genomes]
rs1794038	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2236914	0.85[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2236915	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2793461	0.90[EUR][1000 genomes]
rs2855559	0.90[EUR][1000 genomes]
rs2855560	0.90[EUR][1000 genomes]
rs2855564	0.89[EUR][1000 genomes]
rs4653470	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs6759	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7530245	0.81[EUR][1000 genomes]
rs7530370	0.84[EUR][1000 genomes]
rs8383	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2246221	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs2246221	ARF1	cis	cerebellum	SCAN
rs2246221	PSEN2	cis	parietal	SCAN
rs2246221	ZNF74	trans	parietal	SCAN
rs2246221	C1orf95	cis	cerebellum	SCAN
rs2246221	PSEN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
4	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
5	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
7	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:227069400-227087800	Weak transcription	HMEC	breast
13	chr1:227069400-227102800	Weak transcription	K562	blood
14	chr1:227070000-227076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:227070400-227079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
18	chr1:227071000-227076000	Weak transcription	NHEK	skin
19	chr1:227071000-227077400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:227071200-227075600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:227071200-227075600	Genic enhancers	Lung	lung
23	chr1:227071200-227076000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
25	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
26	chr1:227071200-227091400	Weak transcription	Osteobl	bone
27	chr1:227071400-227076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:227071400-227079000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:227071400-227079600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:227071400-227080000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
32	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:227071800-227078000	Weak transcription	NHLF	lung
34	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
35	chr1:227072000-227075600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
38	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
39	chr1:227072400-227075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:227072800-227077800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:227073000-227078800	Strong transcription	HSMMtube	muscle
43	chr1:227073000-227080400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:227073200-227075800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:227073200-227076200	Weak transcription	A549	lung
47	chr1:227073200-227079600	Weak transcription	Thymus	Thymus
48	chr1:227073400-227075600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:227073400-227075800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:227073400-227076400	Weak transcription	Aorta	Aorta

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