Variant report

Variant	rs681311
Chromosome Location	chr11:120976413-120976414
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	chr11:120975216..120977193-chr11:121456635..121459591,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1783777	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1783778	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1784281	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3016242	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504626	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs538741	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs538936	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs592529	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs638775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638903	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs684384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv524	chr11:120963503-121008167	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs681311	IFT46	cis	cerebellum	SCAN
rs681311	TMPRSS4	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120942800-120979000	Weak transcription	Aorta	Aorta
2	chr11:120958800-120980600	Weak transcription	Brain Germinal Matrix	brain
3	chr11:120971800-120983600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:120974600-120976800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:120974600-120978200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:120975000-120976600	Enhancers	Left Ventricle	heart
7	chr11:120975000-120976600	Enhancers	Right Atrium	heart
8	chr11:120975000-120977200	Enhancers	Fetal Lung	lung
9	chr11:120975000-120977200	Enhancers	Fetal Stomach	stomach
10	chr11:120975000-120977200	Enhancers	Ovary	ovary
11	chr11:120975200-120976600	Enhancers	Adipose Nuclei	Adipose
12	chr11:120975200-120976600	Enhancers	Lung	lung
13	chr11:120975200-120976800	Enhancers	Psoas Muscle	Psoas
14	chr11:120975200-120977600	Enhancers	Fetal Muscle Leg	muscle
15	chr11:120975400-120976800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr11:120975400-120979400	Weak transcription	Spleen	Spleen
17	chr11:120975600-120976600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:120975600-120976600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:120975600-120976600	Active TSS	Fetal Brain Male	brain
20	chr11:120975600-120976600	Enhancers	Rectal Smooth Muscle	rectum
21	chr11:120975600-120977200	Enhancers	Fetal Kidney	kidney
22	chr11:120975800-120977200	Enhancers	Colon Smooth Muscle	Colon
23	chr11:120975800-121005600	Weak transcription	Right Ventricle	heart
24	chr11:120976000-120976600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr11:120976000-120976600	Enhancers	HSMMtube	muscle
26	chr11:120976200-120976600	Enhancers	Brain Anterior Caudate	brain
27	chr11:120976200-120976600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:120976200-120976600	Enhancers	Brain Substantia Nigra	brain
29	chr11:120976200-120976600	Enhancers	Duodenum Mucosa	Duodenum
30	chr11:120976200-120976600	Enhancers	Fetal Intestine Small	intestine
31	chr11:120976200-120976600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr11:120976400-120976600	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:120976400-120976600	Enhancers	Stomach Smooth Muscle	stomach
34	chr11:120976400-120976600	Enhancers	HSMM	muscle
35	chr11:120976400-120984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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