Variant report

Variant	rs2115941
Chromosome Location	chr3:158499695-158499696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:158499248-158499838	K562	blood:	n/a	n/a
2	TCF7L2	chr3:158499561-158500575	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158493881..158495669-chr3:158497844..158499799,2	K562	blood:
2	chr3:158489358..158491459-chr3:158497212..158500197,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271778	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1006911	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1346834	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17699456	0.85[YRI][hapmap]
rs1864508	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2364927	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615052	0.99[ASN][1000 genomes]
rs4680460	0.90[YRI][hapmap]
rs4680467	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57932243	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441224	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6441225	0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6802315	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6802844	0.88[AFR][1000 genomes]
rs6804249	0.95[MKK][hapmap];0.95[YRI][hapmap]
rs7615751	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618110	0.88[ASN][1000 genomes]
rs7635993	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9822005	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861938	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9863103	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881462	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2115941	GFM1	cis	cerebellum	SCAN
rs2115941	LXN	cis	lymphoblastoid	seeQTL
rs2115941	TIPARP	cis	cerebellum	SCAN
rs2115941	MLF1	cis	Heart Left Ventricle	GTEx
rs2115941	LXN	cis	cerebellum	SCAN
rs2115941	RARRES1	cis	cerebellum	SCAN
rs2115941	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs2115941	LXN	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158486800-158518200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:158488400-158501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:158489200-158508800	Weak transcription	Primary T cells from cord blood	blood
4	chr3:158489800-158500600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:158490000-158501000	Weak transcription	Ovary	ovary
6	chr3:158492200-158510600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:158493800-158501400	Weak transcription	Fetal Stomach	stomach
8	chr3:158494600-158501000	Weak transcription	Right Atrium	heart
9	chr3:158494600-158504600	Weak transcription	Left Ventricle	heart
10	chr3:158495400-158505600	Weak transcription	Colonic Mucosa	Colon
11	chr3:158495600-158501200	Weak transcription	Small Intestine	intestine
12	chr3:158495600-158504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:158495600-158508600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:158495800-158499800	Weak transcription	A549	lung
15	chr3:158495800-158501000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:158496000-158500400	Weak transcription	NHLF	lung
17	chr3:158496000-158506000	Weak transcription	Osteobl	bone
18	chr3:158498400-158501600	Enhancers	Fetal Intestine Large	intestine
19	chr3:158498600-158501200	Enhancers	Fetal Intestine Small	intestine
20	chr3:158499000-158499800	Enhancers	K562	blood
21	chr3:158499000-158501600	Enhancers	Fetal Lung	lung
22	chr3:158499200-158501600	Enhancers	Colon Smooth Muscle	Colon
23	chr3:158499400-158500000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr3:158499400-158500200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:158499400-158501600	Enhancers	Fetal Kidney	kidney
26	chr3:158499600-158499800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:158499600-158501600	Enhancers	Rectal Smooth Muscle	rectum

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