Variant report

Variant	rs972798
Chromosome Location	chr12:11874695-11874696
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	chr12:11866674..11868220-chr12:11873125..11875611,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1009951	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs1009953	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs10743967	0.84[EUR][1000 genomes]
rs10845407	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845408	0.92[ASW][hapmap];0.81[CEU][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10845410	0.88[AMR][1000 genomes]
rs11054421	0.88[EUR][1000 genomes]
rs11054423	0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11054424	0.88[EUR][1000 genomes]
rs11054425	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.89[ASN][1000 genomes]
rs11054429	0.89[EUR][1000 genomes]
rs11054433	0.83[EUR][1000 genomes]
rs11054439	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs11615175	0.84[YRI][hapmap]
rs12228191	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12369491	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12828066	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs17818461	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs17818498	0.92[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17818624	0.83[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2051525	0.82[EUR][1000 genomes]
rs2187641	0.92[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2187642	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2416882	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2416883	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]
rs2724588	0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2724599	0.88[EUR][1000 genomes]
rs2724600	0.82[EUR][1000 genomes]
rs2724616	0.89[EUR][1000 genomes]
rs2724618	0.83[EUR][1000 genomes]
rs2724645	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2724648	0.88[EUR][1000 genomes]
rs2856321	0.87[EUR][1000 genomes]
rs2856322	0.83[EUR][1000 genomes]
rs2856324	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs2856338	0.92[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2856344	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2860431	0.92[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2900208	0.81[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2954980	0.88[EUR][1000 genomes]
rs4763719	0.89[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs4763720	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4763721	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7488701	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs762717	0.89[CEU][hapmap];0.86[TSI][hapmap];0.94[EUR][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
rs972798	NECAP1	cis	cerebellum	SCAN

Chromatin state (count:109 , 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	chr12:11861800-11876200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:11865200-11879400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:11865800-11879800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:11869400-11877400	Enhancers	HUVEC	blood vessel
8	chr12:11870200-11885000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:11870400-11879600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:11870600-11875800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:11870600-11876400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:11870800-11877000	Weak transcription	Colonic Mucosa	Colon
13	chr12:11870800-11879800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:11870800-11879800	Weak transcription	Fetal Kidney	kidney
15	chr12:11872000-11875400	Weak transcription	HepG2	liver
16	chr12:11872200-11880200	Weak transcription	Fetal Brain Male	brain
17	chr12:11872400-11877000	Weak transcription	Dnd41	blood
18	chr12:11872800-11875000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:11872800-11875200	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:11872800-11875600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:11872800-11875600	Weak transcription	Fetal Intestine Large	intestine
22	chr12:11872800-11876600	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:11872800-11878000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:11872800-11879400	Weak transcription	Primary T cells from cord blood	blood
25	chr12:11872800-11880000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:11873000-11875000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:11873000-11875200	Weak transcription	Psoas Muscle	Psoas
28	chr12:11873000-11875600	Weak transcription	Stomach Mucosa	stomach
29	chr12:11873000-11876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:11873000-11876400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:11873000-11876600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:11873000-11876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:11873000-11876600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:11873000-11876600	Weak transcription	Fetal Lung	lung
35	chr12:11873000-11876600	Weak transcription	Left Ventricle	heart
36	chr12:11873000-11876600	Weak transcription	Right Atrium	heart
37	chr12:11873000-11876800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:11873000-11876800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:11873000-11876800	Weak transcription	Esophagus	oesophagus
40	chr12:11873000-11876800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:11873000-11876800	Weak transcription	Lung	lung
42	chr12:11873000-11876800	Weak transcription	Pancreas	Pancrea
43	chr12:11873000-11876800	Weak transcription	Right Ventricle	heart
44	chr12:11873000-11877000	Weak transcription	Placenta	Placenta
45	chr12:11873000-11877200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:11873000-11879000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:11873000-11882000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:11873000-11882800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:11873200-11874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:11873200-11874800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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