Variant report

Variant	rs41624
Chromosome Location	chr7:120435638-120435639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120425607..120427372-chr7:120434599..120436896,2	K562	blood:
2	chr7:120435241..120438206-chr7:120589721..120591272,2	MCF-7	breast:
3	chr7:120378952..120380613-chr7:120434028..120436380,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10225453	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10266755	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10274689	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10279837	0.83[ASN][1000 genomes]
rs11982493	0.83[ASN][1000 genomes]
rs12154976	0.91[CEU][hapmap]
rs12669167	0.91[ASN][1000 genomes]
rs13231854	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17142976	0.82[CEU][hapmap]
rs17142995	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1859316	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1859319	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2097806	0.81[CHB][hapmap]
rs2107275	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2189974	0.91[CEU][hapmap]
rs2248890	0.81[JPT][hapmap]
rs2721341	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2721343	0.81[ASN][1000 genomes]
rs2721347	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2721354	0.86[JPT][hapmap]
rs3735467	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3779389	0.86[CHD][hapmap]
rs3823859	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs3823861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41611	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41613	0.81[EUR][1000 genomes]
rs41616	0.81[EUR][1000 genomes]
rs41617	0.82[EUR][1000 genomes]
rs41619	0.93[EUR][1000 genomes]
rs41620	0.94[EUR][1000 genomes]
rs41621	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41622	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs41623	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs41626	0.83[EUR][1000 genomes]
rs41627	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41628	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41631	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs41632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4445165	0.97[ASN][1000 genomes]
rs4730982	0.95[CEU][hapmap]
rs55855220	0.91[ASN][1000 genomes]
rs6466759	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6466760	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6466761	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs6466762	0.95[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs6953454	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6958947	0.86[ASN][1000 genomes]
rs6959328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6961583	0.83[ASN][1000 genomes]
rs6964667	0.89[ASN][1000 genomes]
rs6964786	0.91[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6979247	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs714259	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs727228	0.81[CHB][hapmap]
rs73427866	0.84[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7781985	0.95[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7805211	0.91[ASN][1000 genomes]
rs7805733	0.86[CEU][hapmap]
rs996903	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.91[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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41624	TSPAN12	cis	Artery Tibial	GTEx
rs41624	FLJ21986	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120423000-120449200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:120425800-120437600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:120426600-120442000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
7	chr7:120427800-120438400	Weak transcription	Aorta	Aorta
8	chr7:120428400-120440400	Weak transcription	Fetal Intestine Small	intestine
9	chr7:120429200-120445600	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:120429400-120437200	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:120430200-120437200	Weak transcription	Liver	Liver
12	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:120432400-120436000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:120432400-120442200	Weak transcription	Right Ventricle	heart
15	chr7:120432600-120437200	Weak transcription	Fetal Intestine Large	intestine
16	chr7:120432600-120438000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:120432600-120438200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:120432600-120438800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:120432600-120444600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:120432600-120453800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:120432600-120455400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:120432600-120468400	Weak transcription	Lung	lung
23	chr7:120432800-120435800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:120432800-120438800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:120433200-120437000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:120433200-120446000	Weak transcription	Fetal Kidney	kidney
27	chr7:120434600-120436200	Weak transcription	Left Ventricle	heart
28	chr7:120434800-120436000	Weak transcription	Fetal Heart	heart

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