Variant report

Variant	rs3768445
Chromosome Location	chr1:172362949-172362950
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172327680..172330506-chr1:172362622..172365988,3	MCF-7	breast:
2	chr1:172355733..172358323-chr1:172360920..172363821,3	K562	blood:
3	chr1:172362133..172365037-chr1:172367213..172368755,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-2	chr1:172362654-172363550	NONHSAT007614
2	lnc-PIGC-2	chr1:172362274-172363550	NONHSAT007613

Variant related genes	Relation type
ENSG00000197959	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1011731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1023479	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10752943	0.92[ASN][1000 genomes]
rs10752944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10797996	0.93[ASN][1000 genomes]
rs10911654	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911681	0.98[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10911792	0.90[CHB][hapmap]
rs12404665	0.93[ASN][1000 genomes]
rs12405515	0.87[ASN][1000 genomes]
rs1894633	0.89[CHB][hapmap]
rs2001127	0.97[ASN][1000 genomes]
rs2001128	0.97[ASN][1000 genomes]
rs2001129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213732	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2227199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2227200	0.92[ASN][1000 genomes]
rs2269612	0.93[ASN][1000 genomes]
rs2301453	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3213564	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4504922	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.95[ASN][1000 genomes]
rs4916251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916252	0.93[ASN][1000 genomes]
rs4916253	0.97[ASN][1000 genomes]
rs4916254	0.89[ASN][1000 genomes]
rs4916263	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916264	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916265	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs6424894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6676665	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6700575	0.98[ASN][1000 genomes]
rs714515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73046851	0.80[ASN][1000 genomes]
rs7517737	0.90[ASN][1000 genomes]
rs7518039	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7539464	0.97[ASN][1000 genomes]
rs7539972	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7544610	1.00[ASN][1000 genomes]
rs7546252	0.97[ASN][1000 genomes]
rs9286854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.89[CHB][hapmap]
rs9425297	0.95[ASN][1000 genomes]
rs9425298	0.97[ASN][1000 genomes]
rs9425299	0.97[ASN][1000 genomes]
rs9425300	0.97[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9425575	0.80[ASN][1000 genomes]
rs9425579	0.95[ASN][1000 genomes]
rs9425586	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425587	0.93[ASN][1000 genomes]
rs9425589	0.93[ASN][1000 genomes]
rs9425590	0.94[ASN][1000 genomes]
rs9425591	0.97[ASN][1000 genomes]
rs9425592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs991790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3768445	KIFAP3	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:172349800-172363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:172351400-172363000	Weak transcription	A549	lung
4	chr1:172351800-172363400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:172352200-172363200	Weak transcription	Fetal Intestine Large	intestine
6	chr1:172352400-172386400	Weak transcription	Psoas Muscle	Psoas
7	chr1:172353600-172366400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:172354600-172364000	Weak transcription	Fetal Brain Female	brain
9	chr1:172355000-172363800	Weak transcription	Lung	lung
10	chr1:172355600-172364000	Weak transcription	Fetal Brain Male	brain
11	chr1:172356600-172367400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:172359800-172363400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:172359800-172363600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:172360000-172363200	Enhancers	Brain Hippocampus Middle	brain
15	chr1:172360000-172363400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:172360000-172368200	Weak transcription	HepG2	liver
17	chr1:172360200-172363400	Weak transcription	Esophagus	oesophagus
18	chr1:172360200-172363400	Weak transcription	Fetal Lung	lung
19	chr1:172360200-172363400	Weak transcription	Placenta	Placenta
20	chr1:172360200-172363400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:172360200-172363400	Weak transcription	HSMM	muscle
22	chr1:172360200-172364200	Enhancers	Fetal Kidney	kidney
23	chr1:172360200-172368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:172360200-172369200	Weak transcription	Spleen	Spleen
25	chr1:172360400-172363200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:172360400-172363200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:172360400-172363400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:172360400-172363400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:172360400-172363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:172360400-172363400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:172360400-172363400	Weak transcription	Right Atrium	heart
32	chr1:172360400-172363400	Enhancers	NHDF-Ad	bronchial
33	chr1:172360600-172363000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:172360600-172363400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:172360600-172363400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:172360600-172369000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:172360600-172369200	Weak transcription	Small Intestine	intestine
38	chr1:172360800-172363200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:172360800-172363200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:172360800-172363200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:172360800-172363200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:172360800-172363200	Enhancers	Primary B cells from cord blood	blood
43	chr1:172360800-172363200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:172360800-172363200	Weak transcription	HUVEC	blood vessel
45	chr1:172360800-172363200	Weak transcription	Osteobl	bone
46	chr1:172360800-172363400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:172360800-172363400	Weak transcription	NHEK	skin
48	chr1:172360800-172365400	Enhancers	Primary B cells from peripheral blood	blood
49	chr1:172361000-172363200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:172361000-172363200	Weak transcription	Fetal Stomach	stomach

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