Variant report

Variant	rs2403197
Chromosome Location	chr14:104053764-104053765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10431750	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459574	0.85[ASN][1000 genomes]
rs11844466	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11846404	0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11851000	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11851616	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12884809	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12887734	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12889403	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889721	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12889731	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12890820	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12892038	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12894729	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273175	0.95[JPT][hapmap];0.91[MEX][hapmap]
rs2274267	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296482	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2403196	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2896487	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212090	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs34026011	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34186780	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34843146	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34896432	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35026580	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35229468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35496194	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35498576	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4525427	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4900590	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4900591	1.00[YRI][hapmap]
rs4906335	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4906336	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906337	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906338	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4906347	0.83[AMR][1000 genomes]
rs4906350	0.83[AFR][1000 genomes]
rs4906356	0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs55751606	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57072546	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58033365	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60249782	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67899457	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140568	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71417868	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71417869	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7148456	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729438	0.86[ASW][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8017628	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8017993	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2403197	C14orf153	cis	parietal	SCAN
rs2403197	C14orf177	cis	parietal	SCAN
rs2403197	MARK3	cis	cerebellum	SCAN
rs2403197	ZFYVE21	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104035400-104060400	Weak transcription	Fetal Brain Male	brain
3	chr14:104041000-104059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:104041000-104063200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:104041600-104056200	Weak transcription	K562	blood
6	chr14:104041600-104056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:104041800-104059600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:104041800-104060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr14:104042200-104057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr14:104043400-104056600	Weak transcription	Fetal Heart	heart
11	chr14:104043800-104055400	Weak transcription	Brain Angular Gyrus	brain
12	chr14:104043800-104058200	Strong transcription	Fetal Stomach	stomach
13	chr14:104043800-104059600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:104043800-104060200	Weak transcription	Stomach Mucosa	stomach
15	chr14:104044000-104055000	Weak transcription	Colon Smooth Muscle	Colon
16	chr14:104044000-104056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:104045200-104059600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr14:104045400-104054600	Weak transcription	Ovary	ovary
19	chr14:104045400-104055200	Weak transcription	A549	lung
20	chr14:104045600-104054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr14:104045600-104054800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:104045600-104054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:104045600-104055200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr14:104045600-104055200	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:104045600-104055400	Weak transcription	Left Ventricle	heart
26	chr14:104045600-104055400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:104045600-104057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr14:104045600-104057200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:104045600-104059400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:104045600-104060000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr14:104045600-104060000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr14:104045600-104060000	Weak transcription	Fetal Kidney	kidney
33	chr14:104045600-104060400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:104045600-104060600	Weak transcription	NHDF-Ad	bronchial
35	chr14:104045600-104067200	Weak transcription	Primary B cells from cord blood	blood
36	chr14:104045800-104055000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr14:104045800-104056400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:104045800-104059800	Weak transcription	HUVEC	blood vessel
39	chr14:104045800-104060400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr14:104045800-104064200	Weak transcription	Hela-S3	cervix
41	chr14:104046400-104059400	Weak transcription	GM12878-XiMat	blood
42	chr14:104047800-104056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:104048000-104054800	Weak transcription	Fetal Thymus	thymus
44	chr14:104048000-104055400	Weak transcription	Brain Anterior Caudate	brain
45	chr14:104048200-104054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr14:104048200-104054600	Weak transcription	Osteobl	bone
47	chr14:104048200-104055000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr14:104048200-104059800	Weak transcription	NH-A	brain
49	chr14:104048400-104054200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr14:104048400-104054800	Weak transcription	HSMM	muscle

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