Variant report

Variant	rs7349251
Chromosome Location	chr2:152803129-152803130
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	chr2:152713454..152716403-chr2:152801986..152803822,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10208254	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1105617	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12465422	0.92[CHB][hapmap]
rs12470410	0.92[CHB][hapmap]
rs12471646	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12472173	0.86[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12479128	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12992504	0.86[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13011110	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13394161	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs1401780	0.82[JPT][hapmap]
rs1519708	0.92[CHB][hapmap]
rs1519712	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1519713	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1543197	0.85[EUR][1000 genomes]
rs17270332	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17326047	0.83[MEX][hapmap]
rs2001435	0.82[EUR][1000 genomes]
rs2461835	0.82[JPT][hapmap]
rs35343813	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];1.00[MEX][hapmap];0.97[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]
rs36052741	0.80[AMR][1000 genomes]
rs3892133	0.83[EUR][1000 genomes]
rs4524119	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4664067	0.82[JPT][hapmap]
rs4664508	1.00[JPT][hapmap]
rs4664514	0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4664523	0.92[CHB][hapmap]
rs6433727	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433733	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6708698	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6718430	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6719674	0.92[CHB][hapmap]
rs6720927	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6727569	0.92[CHB][hapmap];0.83[MEX][hapmap]
rs6727592	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6729612	0.84[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6729655	0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs6734642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736449	0.92[CHB][hapmap]
rs6745978	0.92[CHB][hapmap]
rs6751763	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6755890	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6756595	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7558481	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7564060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564177	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs7565405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571637	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582231	0.83[MEX][hapmap]
rs7584868	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602165	0.86[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7607621	0.84[EUR][1000 genomes]
rs952340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs956745	0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7349251	FMNL2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152792800-152803200	Weak transcription	Brain Angular Gyrus	brain
2	chr2:152794400-152803600	Weak transcription	Psoas Muscle	Psoas
3	chr2:152799600-152804800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:152799800-152804200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:152799800-152804800	Enhancers	HMEC	breast
6	chr2:152800000-152804000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:152800200-152804000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:152800400-152803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:152801200-152805000	Enhancers	Placenta	Placenta
10	chr2:152801800-152804000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:152801800-152804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:152801800-152805000	Enhancers	NHEK	skin
13	chr2:152802000-152809800	Weak transcription	HepG2	liver
14	chr2:152802400-152803600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:152802800-152803600	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr2:152802800-152803800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:152802800-152803800	Enhancers	Brain Hippocampus Middle	brain
18	chr2:152802800-152804400	Enhancers	Fetal Brain Male	brain
19	chr2:152802800-152805000	Enhancers	Fetal Muscle Leg	muscle
20	chr2:152802800-152805000	Enhancers	Fetal Thymus	thymus
21	chr2:152803000-152803200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:152803000-152803600	Enhancers	Adipose Nuclei	Adipose
23	chr2:152803000-152803600	Enhancers	Fetal Brain Female	brain
24	chr2:152803000-152803600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr2:152803000-152804000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:152803000-152804000	Enhancers	Aorta	Aorta
27	chr2:152803000-152804000	Weak transcription	Esophagus	oesophagus
28	chr2:152803000-152805400	Enhancers	Brain Substantia Nigra	brain

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