Variant report

Variant	rs35124
Chromosome Location	chr12:46279068-46279069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46122710..46125113-chr12:46278918..46282983,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10880841	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs10880853	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs11183166	0.94[CEU][hapmap]
rs12423797	0.88[AFR][1000 genomes]
rs12426716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes]
rs1291625	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1291628	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1366023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1427749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17712809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17774927	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs183646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs2114844	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs2188119	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs247927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs4768662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4768671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582578	0.93[CEU][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299892	0.92[ASN][1000 genomes]
rs7309711	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73097309	0.81[EUR][1000 genomes]
rs73097315	0.82[EUR][1000 genomes]
rs73097319	0.83[EUR][1000 genomes]
rs764192	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961085	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973329	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975444	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv558782	chr12:46254995-46286683	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35124	NELL2	cis	cerebellum	SCAN
rs35124	PDZRN4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46246000-46285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:46246600-46285400	Weak transcription	NH-A	brain
4	chr12:46246600-46285600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:46246600-46286000	Weak transcription	HMEC	breast
6	chr12:46246800-46288000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:46248000-46279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:46248000-46279600	Weak transcription	Gastric	stomach
9	chr12:46251800-46283400	Strong transcription	Fetal Thymus	thymus
10	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:46269000-46279400	Weak transcription	Pancreas	Pancrea
12	chr12:46269000-46287000	Weak transcription	Esophagus	oesophagus
13	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
14	chr12:46269200-46289000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
16	chr12:46269600-46285600	Weak transcription	HSMM	muscle
17	chr12:46269600-46285600	Weak transcription	HSMMtube	muscle
18	chr12:46269600-46285800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:46269600-46287800	Weak transcription	Colonic Mucosa	Colon
20	chr12:46269800-46285800	Weak transcription	Fetal Kidney	kidney
21	chr12:46269800-46285800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:46269800-46285800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:46270000-46279200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:46270000-46279200	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:46270000-46287200	Weak transcription	Osteobl	bone
27	chr12:46270200-46279400	Weak transcription	Left Ventricle	heart
28	chr12:46270200-46285800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:46270600-46279200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:46271200-46279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:46271200-46285400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:46271200-46285600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:46271400-46285800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:46272800-46285600	Weak transcription	HUVEC	blood vessel
35	chr12:46273000-46281200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:46273400-46285600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:46273400-46307600	Weak transcription	NHLF	lung
38	chr12:46273400-46310200	Weak transcription	Stomach Mucosa	stomach
39	chr12:46273400-46311200	Weak transcription	Right Ventricle	heart
40	chr12:46273400-46314400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:46273600-46286000	Weak transcription	Brain Anterior Caudate	brain
42	chr12:46273800-46279200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:46273800-46282200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:46273800-46285400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:46274400-46280600	Strong transcription	Primary T cells from cord blood	blood
46	chr12:46274600-46288000	Weak transcription	Brain Germinal Matrix	brain
47	chr12:46274800-46285200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:46275000-46288600	Weak transcription	Fetal Heart	heart
49	chr12:46275200-46282000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:46275200-46290000	Weak transcription	Fetal Brain Male	brain

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