Variant report

Variant	rs11810417
Chromosome Location	chr1:227398597-227398598
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227396969..227399919-chr1:227412592..227414970,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11802565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807166	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807511	1.00[AMR][1000 genomes]
rs11807555	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807766	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808055	1.00[EUR][1000 genomes]
rs11808370	1.00[EUR][1000 genomes]
rs11808613	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808962	1.00[MEX][hapmap]
rs1355816	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846993	0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847106	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847506	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34413322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35099852	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4364839	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4495663	0.86[ASW][hapmap];0.83[MKK][hapmap]
rs56168464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57660509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57717956	1.00[EUR][1000 genomes]
rs57895961	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58077821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59396012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59523055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60039374	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60423930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60906739	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61494318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61588040	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688385	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs6696713	1.00[ASW][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs6699740	1.00[EUR][1000 genomes]
rs73086744	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73087695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088692	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092512	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094390	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73096314	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098345	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098350	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102326	1.00[EUR][1000 genomes]
rs73102327	1.00[EUR][1000 genomes]
rs73102341	1.00[EUR][1000 genomes]
rs73102913	1.00[AMR][1000 genomes]
rs73102948	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102965	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411165	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140237	1.00[AMR][1000 genomes]
rs74143320	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11810417	PSEN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:227343200-227400400	Weak transcription	A549	lung
3	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
6	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
10	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
14	chr1:227375600-227410800	Weak transcription	HepG2	liver
15	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
16	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
17	chr1:227379600-227399200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:227380200-227405200	Weak transcription	Gastric	stomach
20	chr1:227380200-227421800	Weak transcription	Ovary	ovary
21	chr1:227380400-227400000	Weak transcription	HSMMtube	muscle
22	chr1:227380400-227400000	Weak transcription	NHEK	skin
23	chr1:227380400-227404000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:227380400-227406800	Weak transcription	NHDF-Ad	bronchial
25	chr1:227381600-227406600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:227385000-227400000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
30	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:227386800-227399400	Weak transcription	HUVEC	blood vessel
32	chr1:227386800-227406600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
36	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227397000-227406800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:227397400-227399800	Weak transcription	Fetal Brain Male	brain
39	chr1:227397400-227399800	Weak transcription	NH-A	brain
40	chr1:227397800-227398800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:227397800-227399400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227397800-227399800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:227397800-227400400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:227397800-227400400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227398000-227398800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
46	chr1:227398000-227398800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:227398000-227398800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:227398000-227399000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:227398000-227399000	Strong transcription	Liver	Liver
50	chr1:227398000-227399200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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