Variant report

Variant	rs6715843
Chromosome Location	chr2:153216587-153216588
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	chr2:153190296..153193237-chr2:153215278..153217205,2	MCF-7	breast:
2	chr2:153215582..153217923-chr2:153232272..153234724,2	K562	blood:

Variant related genes	Relation type
ENSG00000157827	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10432492	0.91[MEX][hapmap]
rs10931067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931069	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674872	0.91[MEX][hapmap]
rs12478426	0.91[MEX][hapmap]
rs13022419	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024533	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13029771	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418748	0.82[JPT][hapmap]
rs13419000	0.83[JPT][hapmap]
rs16831028	0.80[MEX][hapmap]
rs2345873	0.82[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs2345903	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28510143	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3890370	0.82[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs4425036	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4547483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664103	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4664106	0.80[MEX][hapmap]
rs4664569	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4664570	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4664573	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58092541	0.96[ASN][1000 genomes]
rs62179530	0.92[ASN][1000 genomes]
rs62179556	0.95[ASN][1000 genomes]
rs6433984	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704965	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725656	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6725789	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754501	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757219	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9288090	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693435	chr2:153210444-153219178	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6715843	FMNL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153194200-153224400	Weak transcription	Aorta	Aorta
2	chr2:153196000-153224800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:153200600-153225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:153200800-153222000	Weak transcription	Placenta	Placenta
5	chr2:153200800-153225800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:153202400-153219800	Weak transcription	Hela-S3	cervix
7	chr2:153202400-153225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:153203000-153223800	Weak transcription	Fetal Stomach	stomach
9	chr2:153203000-153233000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:153205400-153223800	Weak transcription	HMEC	breast
11	chr2:153206800-153240800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:153207000-153223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
14	chr2:153209400-153237000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:153209800-153225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:153210800-153223200	Weak transcription	Ovary	ovary
17	chr2:153211000-153223200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:153212000-153218200	Weak transcription	NH-A	brain
19	chr2:153212000-153223600	Weak transcription	NHEK	skin
20	chr2:153212000-153224200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:153212400-153218000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:153212400-153224200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:153212800-153219400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:153212800-153225600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:153213400-153219400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:153213400-153221600	Weak transcription	Psoas Muscle	Psoas
27	chr2:153214800-153223800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:153214800-153227600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:153215000-153226000	Weak transcription	Left Ventricle	heart
30	chr2:153215600-153224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:153215800-153216800	Enhancers	A549	lung
32	chr2:153215800-153217200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:153216000-153216600	Enhancers	Fetal Lung	lung
34	chr2:153216000-153216800	Enhancers	Osteobl	bone
35	chr2:153216000-153217000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:153216200-153217000	Enhancers	Brain Hippocampus Middle	brain
37	chr2:153216200-153217600	Enhancers	HepG2	liver
38	chr2:153216400-153216600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:153216400-153216800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:153216400-153217200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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