Variant report

Variant	rs1430351
Chromosome Location	chr2:73330954-73330955
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	chr2:73330344..73333243-chr2:73334640..73337340,3	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10166220	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10167566	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10174548	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10176939	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10177159	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs10180720	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10180995	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10189744	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10190861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192077	0.83[ASW][hapmap];0.87[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10197305	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs10203608	0.93[ASN][1000 genomes]
rs10209859	0.81[CEU][hapmap]
rs1046186	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865396	0.89[ASN][1000 genomes]
rs11126389	0.89[ASN][1000 genomes]
rs11686557	0.94[ASN][1000 genomes]
rs11885522	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12104691	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12233055	0.87[CEU][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs12614059	0.91[ASN][1000 genomes]
rs13018842	0.89[ASN][1000 genomes]
rs13385994	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13388404	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs13390072	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13391532	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393567	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13400920	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13400948	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13403757	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13403781	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13407719	0.92[ASN][1000 genomes]
rs13416407	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13427947	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370383	0.82[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs1430349	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1430350	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008571	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs17008611	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs17008631	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs1992133	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421098	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs35131031	0.86[ASN][1000 genomes]
rs3813222	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813223	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3901273	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4144837	0.93[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs4514897	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4591365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55894650	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57536428	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57701326	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57726945	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57937746	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546796	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs6546797	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs6546800	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546801	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6709938	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs6710739	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs6711891	0.81[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs6712925	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6713655	0.89[EUR][1000 genomes]
rs6719333	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs6720817	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6726940	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs6727269	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6727919	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729266	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs6732369	0.81[CEU][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs6736153	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6749237	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6750069	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs6754779	0.89[EUR][1000 genomes]
rs6754858	0.89[EUR][1000 genomes]
rs6757131	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs6759733	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs727470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs727471	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732178	0.87[CEU][hapmap]
rs732179	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs732180	0.87[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7557173	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7559074	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559340	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7566904	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7570876	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs7579770	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs7580216	0.87[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7593322	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7597032	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs7599657	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602651	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs891432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs891433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs893258	0.86[JPT][hapmap]
rs893259	0.81[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs9309471	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1430351	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73315600-73338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:73316200-73338400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:73316400-73334400	Weak transcription	Fetal Brain Female	brain
4	chr2:73316400-73335000	Weak transcription	Brain Substantia Nigra	brain
5	chr2:73318400-73331800	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:73318600-73334400	Weak transcription	HMEC	breast
7	chr2:73320200-73332200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:73320600-73332800	Weak transcription	Esophagus	oesophagus
9	chr2:73320800-73332800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:73320800-73334400	Weak transcription	Aorta	Aorta
11	chr2:73321600-73332800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:73322400-73334600	Weak transcription	Psoas Muscle	Psoas
13	chr2:73326800-73332000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:73327000-73334400	Strong transcription	Fetal Stomach	stomach
15	chr2:73327000-73338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:73328200-73332800	Enhancers	Spleen	Spleen
17	chr2:73328800-73331200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:73328800-73331200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:73328800-73331200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:73328800-73331200	Enhancers	HUVEC	blood vessel
21	chr2:73328800-73331400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:73329000-73331800	Strong transcription	HepG2	liver
23	chr2:73329000-73333000	Weak transcription	NHEK	skin
24	chr2:73329000-73334800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:73329200-73331000	Enhancers	Fetal Intestine Large	intestine
26	chr2:73329200-73331200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:73329200-73331200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:73329400-73331000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:73329400-73331200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:73329400-73332200	Weak transcription	NHDF-Ad	bronchial
31	chr2:73329400-73332800	Weak transcription	HSMMtube	muscle
32	chr2:73329400-73338200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:73329600-73331400	Enhancers	Hela-S3	cervix
34	chr2:73329600-73331800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr2:73329600-73337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:73329800-73331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:73329800-73334200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:73329800-73334400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:73329800-73337800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:73330000-73331000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:73330000-73331200	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:73330000-73332600	Weak transcription	HSMM	muscle
43	chr2:73330200-73334400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:73330400-73331200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:73330400-73331200	Enhancers	Ovary	ovary
46	chr2:73330400-73331600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:73330400-73332000	Weak transcription	Fetal Heart	heart
48	chr2:73330400-73332800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:73330400-73333400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:73330400-73337400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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