Variant report

Variant	rs10913723
Chromosome Location	chr1:179296055-179296056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179294599..179296608-chr1:179299221..179301081,2	MCF-7	breast:
2	chr1:179294763..179296737-chr1:179297723..179299228,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10913709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913717	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913726	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913769	1.00[CHB][hapmap]
rs11581659	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12061572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066392	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135682	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722736	1.00[CHB][hapmap]
rs12730051	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730056	1.00[ASW][hapmap]
rs12746331	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12755434	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248818	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484442	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493120	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164740	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34315375	0.88[ASN][1000 genomes]
rs4651023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652363	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];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425536	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs68039464	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10913723	NPHS2	cis	cerebellum	SCAN
rs10913723	FAM5B	cis	parietal	SCAN
rs10913723	TOR3A	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179304600	Weak transcription	Lung	lung
2	chr1:179263800-179306400	Weak transcription	Gastric	stomach
3	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
4	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
9	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
11	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
12	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:179274600-179302400	Weak transcription	Left Ventricle	heart
15	chr1:179274600-179304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:179274600-179306000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:179275600-179311600	Weak transcription	HUVEC	blood vessel
18	chr1:179276400-179306200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:179276600-179304800	Weak transcription	Pancreas	Pancrea
20	chr1:179277600-179296400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:179280400-179296200	Weak transcription	NH-A	brain
22	chr1:179280400-179314000	Weak transcription	NHLF	lung
23	chr1:179280600-179299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:179281200-179300200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:179282000-179313000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:179282400-179304200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:179282400-179313800	Weak transcription	HSMMtube	muscle
28	chr1:179283200-179298800	Weak transcription	HepG2	liver
29	chr1:179283200-179308600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:179286400-179313800	Weak transcription	Psoas Muscle	Psoas
31	chr1:179287200-179297200	Weak transcription	Spleen	Spleen
32	chr1:179287400-179304400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:179287600-179299000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:179289000-179299200	Weak transcription	Fetal Stomach	stomach
35	chr1:179290000-179297800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:179290200-179297800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:179290200-179297800	Weak transcription	Fetal Intestine Small	intestine
38	chr1:179290200-179300000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:179290200-179300200	Strong transcription	Hela-S3	cervix
40	chr1:179290400-179310000	Weak transcription	Aorta	Aorta
41	chr1:179290600-179298200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:179290600-179298600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:179290600-179304200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:179290600-179308800	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:179290800-179298600	Weak transcription	A549	lung
46	chr1:179290800-179298800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:179290800-179298800	Weak transcription	Fetal Intestine Large	intestine
48	chr1:179290800-179314000	Weak transcription	NHEK	skin
49	chr1:179291000-179297800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:179291000-179306000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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