Variant report

Variant	rs1196478
Chromosome Location	chr7:121611614-121611615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11767822	0.84[EUR][1000 genomes]
rs1196477	0.83[ASW][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1196480	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196481	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196483	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196484	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196486	0.82[EUR][1000 genomes]
rs1196487	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196488	0.81[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196490	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1196491	0.81[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196493	0.96[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1196494	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196495	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196496	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1196510	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1196511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211621	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12671846	0.83[EUR][1000 genomes]
rs1721857	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1721858	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1721859	0.86[EUR][1000 genomes]
rs1916875	0.83[EUR][1000 genomes]
rs1916876	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2024252	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2690271	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690272	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629793	0.84[EUR][1000 genomes]
rs4731044	0.82[CEU][hapmap];0.83[MEX][hapmap];0.86[EUR][1000 genomes]
rs6961716	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6967270	0.86[EUR][1000 genomes]
rs727766	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7794741	0.82[CEU][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs7810556	0.80[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196478	NKPD1	trans	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:121582600-121617600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:121596000-121618400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:121601600-121628000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:121601800-121625600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:121602000-121614600	Weak transcription	Fetal Brain Female	brain
6	chr7:121602400-121618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:121603400-121631400	Weak transcription	NHEK	skin
8	chr7:121603600-121614800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:121604000-121616600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:121605800-121627600	Weak transcription	Brain Germinal Matrix	brain
11	chr7:121606200-121612000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:121606800-121614800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:121607400-121619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:121607600-121613600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:121607800-121614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:121607800-121617400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:121607800-121625400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:121609400-121613800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:121609600-121614600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:121609800-121612600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:121609800-121613600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:121609800-121614400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:121611200-121618400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:121611400-121612400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:121611400-121618000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:121611600-121621600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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