Variant report

Variant	rs16846798
Chromosome Location	chr1:227192469-227192470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227191783..227193581-chr1:227195403..227197131,2	K562	blood:
2	chr1:227173983..227176329-chr1:227192052..227193578,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11802565	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804315	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804924	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807511	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11807766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808055	1.00[EUR][1000 genomes]
rs11808962	1.00[MEX][hapmap]
rs12562621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12562646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12565025	0.92[ASN][1000 genomes]
rs12565212	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12565685	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12567464	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12567790	1.00[ASN][1000 genomes]
rs12567972	0.96[ASN][1000 genomes]
rs12568014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12569190	0.84[ASN][1000 genomes]
rs12569194	0.84[ASN][1000 genomes]
rs1316851	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16841298	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846716	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846731	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846733	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs16846738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846772	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846779	1.00[ASN][1000 genomes]
rs16846780	1.00[ASN][1000 genomes]
rs16846783	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846790	0.96[ASN][1000 genomes]
rs16846792	0.96[ASN][1000 genomes]
rs16846808	1.00[ASN][1000 genomes]
rs16846811	1.00[ASN][1000 genomes]
rs16846862	0.84[ASN][1000 genomes]
rs16846867	0.84[ASN][1000 genomes]
rs16846903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16846944	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16846993	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847001	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16847020	0.89[CHB][hapmap]
rs16847106	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847137	0.84[ASN][1000 genomes]
rs1888829	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2009053	0.84[ASN][1000 genomes]
rs2297411	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2297417	1.00[ASN][1000 genomes]
rs34413322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35099852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738728	0.96[ASN][1000 genomes]
rs3795450	1.00[ASN][1000 genomes]
rs3795452	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41527149	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4281295	0.84[ASN][1000 genomes]
rs4459073	0.84[ASN][1000 genomes]
rs4521963	0.84[ASN][1000 genomes]
rs55947609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56043893	1.00[ASN][1000 genomes]
rs56168464	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57717956	1.00[EUR][1000 genomes]
rs57895961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58077821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59396012	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59523055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59945801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60107850	0.92[ASN][1000 genomes]
rs61494318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73086744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73087619	1.00[EUR][1000 genomes]
rs73087659	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73087695	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089703	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089763	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091744	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091778	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102913	1.00[AMR][1000 genomes]
rs73102948	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102965	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411165	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140237	1.00[AMR][1000 genomes]
rs74143320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs944601	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs944602	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs961490	0.92[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846798	PSEN2	cis	lymphoblastoid	seeQTL
rs16846798	CDC42BPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227175200-227198400	Weak transcription	A549	lung
3	chr1:227175200-227210200	Weak transcription	HMEC	breast
4	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:227176000-227216400	Weak transcription	NHLF	lung
6	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
7	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
8	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
12	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
13	chr1:227179600-227213800	Weak transcription	NH-A	brain
14	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:227182200-227205600	Weak transcription	Fetal Brain Male	brain
16	chr1:227182600-227206400	Weak transcription	Brain Germinal Matrix	brain
17	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
18	chr1:227183200-227202600	Weak transcription	Pancreas	Pancrea
19	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
21	chr1:227183600-227204600	Weak transcription	HepG2	liver
22	chr1:227183800-227203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227184000-227203200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:227184000-227204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:227184000-227214600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:227184200-227206600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:227184600-227208000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:227187800-227192800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:227187800-227192800	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:227187800-227193400	Strong transcription	HUVEC	blood vessel
33	chr1:227187800-227194800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:227188000-227192800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:227188000-227194600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:227188200-227192800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:227188200-227192800	Strong transcription	Adipose Nuclei	Adipose
38	chr1:227188200-227192800	Strong transcription	Brain Anterior Caudate	brain
39	chr1:227188200-227192800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:227188200-227192800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:227188200-227192800	Strong transcription	Fetal Intestine Large	intestine
42	chr1:227188200-227192800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:227188200-227192800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:227188200-227193000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:227188200-227194400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:227188200-227194400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227188400-227192800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:227188400-227193000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:227188400-227193000	Strong transcription	Fetal Stomach	stomach
50	chr1:227188600-227192800	Strong transcription	Fetal Lung	lung

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