Variant report

Variant	rs3817551
Chromosome Location	chr12:121882098-121882099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 1)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121881699-121882203	HL-60	blood:	n/a	n/a
2	POLR2A	chr12:121880255-121883309	GM12878	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121789115..121791658-chr12:121880840..121882827,2	MCF-7	breast:
2	chr12:121878170..121879977-chr12:121880057..121882687,2	MCF-7	breast:
3	chr12:121871998..121875196-chr12:121881488..121886297,4	K562	blood:
4	chr12:121789271..121791434-chr12:121880187..121882696,2	K562	blood:
5	chr12:121866984..121868948-chr12:121881772..121883367,2	MCF-7	breast:
6	chr12:121733765..121736569-chr12:121879944..121882685,2	MCF-7	breast:
7	chr12:121881613..121883243-chr12:121887047..121889085,2	K562	blood:
8	chr12:121880609..121882704-chr12:121889247..121891009,2	K562	blood:
9	chr12:121880833..121882674-chr12:121883238..121886175,2	MCF-7	breast:
10	chr12:121788278..121791610-chr12:121879889..121884323,6	MCF-7	breast:
11	chr12:121879603..121883744-chr12:121903538..121907174,6	MCF-7	breast:
12	chr12:121880512..121882680-chr12:121974810..121977371,2	MCF-7	breast:
13	chr12:121881127..121882674-chr12:121887819..121890318,2	MCF-7	breast:
14	chr12:121881584..121884550-chr12:121902935..121904495,2	MCF-7	breast:
15	chr12:121836745..121839603-chr12:121879742..121884021,4	MCF-7	breast:
16	chr12:121879600..121882524-chr12:121903519..121905264,3	K562	blood:
17	chr12:121837014..121839501-chr12:121881211..121882781,2	MCF-7	breast:
18	chr12:121881960..121883716-chr12:121885028..121886945,2	K562	blood:

No data

miRNA name	Chromosome Location	mirBase accession
hsa-miR-7107-3p	chr12:121882082-121882108	MIMAT0028112

No data

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000170633	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000110931	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10444489	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10444491	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10444492	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1064951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744763	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10744764	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10774594	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774595	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774596	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774597	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774598	1.00[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10849873	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849875	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849877	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849878	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849879	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849880	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849882	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849884	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849885	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10849888	0.86[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10849889	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849891	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065549	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065551	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065565	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065575	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065576	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065582	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065583	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065585	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11838335	1.00[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12427382	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578785	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581861	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582182	0.80[ASN][1000 genomes]
rs2288154	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817543	1.00[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817544	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817547	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4081775	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4980986	0.84[MEX][hapmap];0.85[MKK][hapmap]
rs4980994	0.84[CHD][hapmap];0.84[MEX][hapmap]
rs57185007	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57889600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57971979	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58609847	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58849369	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59103597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59190874	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61953461	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61953462	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61953497	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61955092	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61955131	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61955132	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61955138	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9300314	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951498	1.00[ASW][hapmap];0.96[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9634167	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9634168	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3817551	NME2P1	cis	cerebellum	SCAN
rs3817551	TMEM120B	cis	cerebellum	SCAN
rs3817551	TAOK3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121850400-121887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:121851800-121891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:121852200-121883200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:121852200-121884800	Strong transcription	Primary T cells from cord blood	blood
5	chr12:121853000-121884800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:121861400-121903600	Weak transcription	Right Atrium	heart
7	chr12:121864000-121889200	Strong transcription	Fetal Intestine Small	intestine
8	chr12:121864200-121883600	Strong transcription	Spleen	Spleen
9	chr12:121864600-121887200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:121865000-121884000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:121867600-121890000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:121868000-121893600	Weak transcription	Psoas Muscle	Psoas
13	chr12:121869600-121886400	Weak transcription	Fetal Heart	heart
14	chr12:121872600-121883400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:121873000-121883800	Strong transcription	Liver	Liver
16	chr12:121873200-121883200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:121873400-121883200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:121873600-121884400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:121874000-121889600	Weak transcription	HMEC	breast
20	chr12:121874400-121882400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:121874600-121882800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:121875000-121882600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:121875000-121883600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:121875000-121883600	Strong transcription	Brain Germinal Matrix	brain
25	chr12:121875000-121884800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:121875000-121886800	Weak transcription	Fetal Brain Male	brain
27	chr12:121875200-121883800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:121875200-121885000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:121875200-121889800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:121875200-121889800	Weak transcription	HUVEC	blood vessel
31	chr12:121875400-121884400	Strong transcription	Fetal Brain Female	brain
32	chr12:121875600-121883400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:121875600-121883400	Strong transcription	Thymus	Thymus
34	chr12:121875600-121883600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:121875600-121883800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:121875600-121883800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:121875600-121884400	Strong transcription	Dnd41	blood
38	chr12:121875600-121889200	Strong transcription	Fetal Thymus	thymus
39	chr12:121876200-121882400	Strong transcription	Gastric	stomach
40	chr12:121876200-121883200	Strong transcription	NHLF	lung
41	chr12:121876200-121883600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:121876400-121884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:121876600-121883400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:121876600-121883600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:121876600-121883600	Strong transcription	GM12878-XiMat	blood
46	chr12:121876800-121883000	Strong transcription	Right Ventricle	heart
47	chr12:121876800-121887400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:121877800-121889800	Weak transcription	NHDF-Ad	bronchial
49	chr12:121878200-121886400	Weak transcription	HSMM	muscle
50	chr12:121878400-121882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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