Variant report

Variant	rs2172402
Chromosome Location	chr3:158351891-158351892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62286643	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62286645	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	13 gene(s)	inside rSNPs	diseases
6	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv999299	chr3:158348460-158358157	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region	2 gene(s)	inside rSNPs	diseases
8	esv3461211	chr3:158348758-158353756	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	inside rSNPs	diseases
9	esv2518941	chr3:158349755-158352064	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
10	esv3461213	chr3:158349783-158353131	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
11	esv3450832	chr3:158350108-158352906	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
12	esv3461217	chr3:158350339-158352232	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
13	esv3461216	chr3:158350610-158351995	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3461212	chr3:158350629-158352011	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers	n/a	n/a	inside rSNPs	diseases
15	esv3351645	chr3:158350645-158351997	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
16	esv3461214	chr3:158350661-158351984	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
17	esv3461215	chr3:158350726-158351916	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
18	esv3528677	chr3:158350736-158351915	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
19	esv1141426	chr3:158350740-158351912	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
20	esv3461218	chr3:158350740-158351913	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
21	esv3528678	chr3:158350740-158351913	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2172402	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs2172402	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158350200-158352000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:158350400-158352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:158350600-158352000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:158350600-158352000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:158350600-158352200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:158351800-158352000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:158351800-158352400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:158351800-158352400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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