Variant report

Variant	rs11715640
Chromosome Location	chr3:121313535-121313536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10222346	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934553	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707840	0.81[YRI][hapmap]
rs11714812	0.82[GIH][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs11715635	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719547	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491882	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs1464100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464101	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4676730	0.81[ASW][hapmap];0.82[GIH][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs4676732	0.81[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs4676735	0.81[AMR][1000 genomes]
rs4676736	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs6438637	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769187	0.81[YRI][hapmap]
rs7631876	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634634	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs898686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858923	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv2757006	chr3:121264886-121323465	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv2759172	chr3:121264886-121323465	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv877382	chr3:121300728-121324643	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv965204	chr3:121305043-121322455	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv10310	chr3:121311716-121313964	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11715640	IQCB1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121311400-121315000	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:121311800-121315200	Enhancers	Liver	Liver
3	chr3:121311800-121315200	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:121312000-121317600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:121312000-121320000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:121312200-121313600	Weak transcription	Adipose Nuclei	Adipose
7	chr3:121312200-121314200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:121312200-121314400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:121312200-121314600	Active TSS	Left Ventricle	heart
10	chr3:121312200-121314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:121312200-121316200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:121312200-121320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:121312400-121314600	Active TSS	Right Atrium	heart
14	chr3:121312400-121320000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:121312600-121313600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:121312600-121315600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:121312600-121320000	Weak transcription	HSMMtube	muscle
18	chr3:121312800-121313800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:121312800-121315000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:121312800-121315000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:121312800-121315800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:121313000-121317400	Weak transcription	Right Ventricle	heart
23	chr3:121313200-121313600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:121313200-121314200	Enhancers	Psoas Muscle	Psoas
25	chr3:121313400-121313600	Flanking Active TSS	Fetal Heart	heart
26	chr3:121313400-121314400	Enhancers	HepG2	liver

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