Variant report

Variant	rs2416883
Chromosome Location	chr12:11876394-11876395
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	chr12:11866545..11868091-chr12:11875142..11877760,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009951	0.92[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1009953	0.92[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs10743967	0.81[EUR][1000 genomes]
rs10845407	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10845408	0.85[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11054421	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs11054423	0.81[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs11054424	0.85[EUR][1000 genomes]
rs11054425	0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs11054429	0.86[EUR][1000 genomes]
rs11054433	0.81[EUR][1000 genomes]
rs11054439	0.89[JPT][hapmap]
rs11615175	0.82[CHB][hapmap]
rs12228191	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12369491	0.92[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs12828066	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap]
rs17818461	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17818498	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17818624	0.81[CEU][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs2187641	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs2187642	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2416882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724588	0.81[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2724599	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2724600	0.81[EUR][1000 genomes]
rs2724616	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs2724618	0.81[EUR][1000 genomes]
rs2724635	0.81[CEU][hapmap]
rs2724645	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2724648	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2856321	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2856322	0.80[EUR][1000 genomes]
rs2856324	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2856338	0.96[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2856344	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2860431	0.96[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2900208	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2954980	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4763719	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4763720	0.97[EUR][1000 genomes]
rs4763721	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7488701	0.97[EUR][1000 genomes]
rs762717	0.92[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs972798	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2416883	NECAP1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11827400-11879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:11848800-11879600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:11857000-11876800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:11865200-11879400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:11865800-11879800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:11869400-11877400	Enhancers	HUVEC	blood vessel
7	chr12:11870200-11885000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:11870400-11879600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:11870600-11876400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:11870800-11877000	Weak transcription	Colonic Mucosa	Colon
11	chr12:11870800-11879800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:11870800-11879800	Weak transcription	Fetal Kidney	kidney
13	chr12:11872200-11880200	Weak transcription	Fetal Brain Male	brain
14	chr12:11872400-11877000	Weak transcription	Dnd41	blood
15	chr12:11872800-11876600	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:11872800-11878000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:11872800-11879400	Weak transcription	Primary T cells from cord blood	blood
18	chr12:11872800-11880000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:11873000-11876400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:11873000-11876600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:11873000-11876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:11873000-11876600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:11873000-11876600	Weak transcription	Fetal Lung	lung
24	chr12:11873000-11876600	Weak transcription	Left Ventricle	heart
25	chr12:11873000-11876600	Weak transcription	Right Atrium	heart
26	chr12:11873000-11876800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:11873000-11876800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:11873000-11876800	Weak transcription	Esophagus	oesophagus
29	chr12:11873000-11876800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:11873000-11876800	Weak transcription	Lung	lung
31	chr12:11873000-11876800	Weak transcription	Pancreas	Pancrea
32	chr12:11873000-11876800	Weak transcription	Right Ventricle	heart
33	chr12:11873000-11877000	Weak transcription	Placenta	Placenta
34	chr12:11873000-11877200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:11873000-11879000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:11873000-11882000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:11873000-11882800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:11873200-11876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:11873200-11876600	Weak transcription	Spleen	Spleen
40	chr12:11873200-11876800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:11873200-11876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:11873200-11876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:11873200-11876800	Weak transcription	Aorta	Aorta
44	chr12:11873200-11876800	Weak transcription	Brain Substantia Nigra	brain
45	chr12:11873200-11876800	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:11873200-11876800	Weak transcription	Fetal Stomach	stomach
47	chr12:11873200-11876800	Weak transcription	Gastric	stomach
48	chr12:11873200-11877000	Weak transcription	Liver	Liver
49	chr12:11873200-11877000	Weak transcription	Brain Angular Gyrus	brain
50	chr12:11873200-11877000	Weak transcription	Brain Anterior Caudate	brain

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