Variant report

Variant	rs13099184
Chromosome Location	chr3:142174416-142174417
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	chr3:142173107..142175736-chr3:142179768..142182228,2	K562	blood:
2	chr3:142165537..142167981-chr3:142173026..142174613,2	K562	blood:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10935460	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs10935463	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129391	0.81[EUR][1000 genomes]
rs11708470	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715514	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11916455	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12629713	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12634255	0.80[EUR][1000 genomes]
rs12638158	0.80[EUR][1000 genomes]
rs12639363	0.81[EUR][1000 genomes]
rs13063075	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13065800	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13066441	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13068397	0.80[EUR][1000 genomes]
rs13070239	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13071750	0.82[CEU][hapmap]
rs13072355	0.80[EUR][1000 genomes]
rs13075259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082648	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs13085247	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13085261	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13089219	0.80[EUR][1000 genomes]
rs13092593	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1485393	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs16852267	0.86[CHB][hapmap]
rs2227929	0.81[EUR][1000 genomes]
rs2227931	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2306699	0.91[CHB][hapmap]
rs34392719	0.82[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap]
rs3762799	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs3923464	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4256152	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs4558780	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4582075	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440085	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6776402	0.81[EUR][1000 genomes]
rs6786320	0.89[CHB][hapmap]
rs6809448	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs7623785	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs7630115	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643377	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs7647329	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs953135	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs9814159	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs9829125	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs9859834	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs9867210	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3523317	chr3:142172020-142176793	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv3523318	chr3:142172020-142176793	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13099184	XRN1	cis	cerebellum	SCAN
rs13099184	PLS1	cis	parietal	SCAN
rs13099184	TRPC1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142174800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:142167200-142174800	Weak transcription	Lung	lung
3	chr3:142167200-142176800	Weak transcription	Gastric	stomach
4	chr3:142167200-142178800	Weak transcription	Small Intestine	intestine
5	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
6	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
7	chr3:142167400-142175600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:142167400-142176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:142167400-142176800	Weak transcription	Placenta	Placenta
10	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
12	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
14	chr3:142167600-142176400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:142167600-142177000	Weak transcription	Right Ventricle	heart
16	chr3:142167600-142177000	Weak transcription	NH-A	brain
17	chr3:142167600-142177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:142167600-142177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:142167600-142177600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:142167600-142180000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:142167600-142180000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:142167600-142187200	Weak transcription	Fetal Brain Male	brain
23	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
24	chr3:142167600-142199600	Weak transcription	Ovary	ovary
25	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
26	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
27	chr3:142167800-142175800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:142167800-142176000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:142167800-142176200	Weak transcription	HUVEC	blood vessel
30	chr3:142167800-142177000	Weak transcription	Brain Anterior Caudate	brain
31	chr3:142167800-142177000	Weak transcription	NHDF-Ad	bronchial
32	chr3:142167800-142177400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:142167800-142177600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:142167800-142177600	Weak transcription	NHEK	skin
35	chr3:142167800-142179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:142167800-142179800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:142167800-142180000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:142167800-142180200	Weak transcription	HepG2	liver
39	chr3:142167800-142184800	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:142167800-142186400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:142167800-142188800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:142167800-142190400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:142168000-142176400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:142168000-142182600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:142168000-142192000	Weak transcription	Fetal Lung	lung
49	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:142168000-142200000	Weak transcription	Fetal Kidney	kidney

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