Variant report

Variant	rs1523785
Chromosome Location	chr2:36737784-36737785
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	chr2:36581721..36584860-chr2:36733374..36737959,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260025	Chromatin interaction
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10180792	0.87[JPT][hapmap]
rs10184223	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11681392	0.88[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11694761	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2287082	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs3755197	0.88[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs3770821	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs3770822	0.80[CEU][hapmap]
rs3770832	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770833	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3815552	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5003670	0.87[JPT][hapmap]
rs6721081	0.83[EUR][1000 genomes]
rs848522	0.89[CHB][hapmap]
rs848523	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs848564	0.89[CHB][hapmap]
rs861050	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1523785	FEZ2	cis	parietal	SCAN
rs1523785	FEZ2	cis	cerebellum	SCAN
rs1523785	CRIM1	cis	cerebellum	SCAN
rs1523785	CDC42EP3	cis	parietal	SCAN
rs1523785	BCAR3	trans	parietal	SCAN
rs1523785	STRN	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36705000-36743200	Weak transcription	Brain Germinal Matrix	brain
2	chr2:36707000-36740600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:36708600-36739000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:36709200-36739000	Weak transcription	Colonic Mucosa	Colon
5	chr2:36710000-36743400	Weak transcription	Primary T cells from cord blood	blood
6	chr2:36711400-36739200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:36713600-36739200	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:36717400-36744400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:36720000-36760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:36720400-36739200	Weak transcription	Fetal Heart	heart
12	chr2:36720800-36739200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:36721800-36746000	Strong transcription	HUVEC	blood vessel
14	chr2:36722400-36739800	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:36722600-36752400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:36724000-36740600	Weak transcription	Psoas Muscle	Psoas
17	chr2:36725200-36739200	Strong transcription	NH-A	brain
18	chr2:36725200-36756800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:36726800-36751800	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:36727000-36739200	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:36727000-36739600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:36727200-36739200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:36727400-36738400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:36727400-36757200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:36727600-36739200	Weak transcription	Fetal Brain Female	brain
26	chr2:36727600-36739200	Weak transcription	Fetal Kidney	kidney
27	chr2:36727600-36739400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:36727600-36739400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:36727600-36739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:36727600-36739800	Weak transcription	Right Ventricle	heart
31	chr2:36727600-36740800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:36727600-36743600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:36728000-36738800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:36728000-36739000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:36728000-36739200	Weak transcription	Fetal Lung	lung
36	chr2:36728000-36739400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:36728400-36749200	Weak transcription	Fetal Brain Male	brain
38	chr2:36729200-36739000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:36729200-36740600	Weak transcription	Liver	Liver
40	chr2:36729400-36738000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:36729400-36738800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:36729400-36739200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:36729600-36739400	Weak transcription	Brain Substantia Nigra	brain
44	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
45	chr2:36730800-36739600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:36731000-36738600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:36731200-36738200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:36731800-36738200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:36732400-36738800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:36733000-36752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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