Variant report

Variant	rs1401180
Chromosome Location	chr11:93694951-93694952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1518567	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1518568	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1518574	0.87[ASW][hapmap];0.88[CEU][hapmap]
rs1518577	0.81[AFR][1000 genomes]
rs1960895	0.92[CEU][hapmap]
rs2174638	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2174640	0.80[EUR][1000 genomes]
rs2203794	0.88[CEU][hapmap]
rs2213109	0.88[CEU][hapmap]
rs2256323	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256426	0.86[ASN][1000 genomes]
rs2456557	0.86[ASN][1000 genomes]
rs2456564	0.90[EUR][1000 genomes]
rs2456565	0.90[EUR][1000 genomes]
rs2462741	0.88[CEU][hapmap]
rs2462742	0.88[CEU][hapmap]
rs2511388	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2511391	0.86[ASN][1000 genomes]
rs2511392	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508650	chr11:93609010-93713576	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1049467	chr11:93651025-93778717	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv442	chr11:93665117-93717973	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv2757466	chr11:93676224-93714950	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759854	chr11:93676224-93714950	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2760207	chr11:93692312-93701588	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3474853	chr11:93693504-93698702	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3474864	chr11:93693504-93698702	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3495079	chr11:93694004-93703302	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3495078	chr11:93694454-93703152	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2511618	chr11:93694604-93702872	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv8864	chr11:93694672-93702559	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv1819337	chr11:93694753-93702531	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1401180	FAT3	cis	parietal	SCAN
rs1401180	HEPHL1	cis	Artery Tibial	GTEx
rs1401180	SRSF8	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93694400-93696000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:93694600-93696400	Enhancers	HMEC	breast
3	chr11:93694600-93696600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:93694800-93695200	Enhancers	Fetal Lung	lung
5	chr11:93694800-93695600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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