Variant report

Variant	rs4899260
Chromosome Location	chr14:69278204-69278205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:69276296..69278428-chr14:69281559..69284109,2	K562	blood:
2	chr14:68713706..68716273-chr14:69277811..69279687,2	MCF-7	breast:
3	chr14:68281799..68283373-chr14:69277019..69279798,2	MCF-7	breast:
4	chr14:68775195..68777940-chr14:69277333..69279325,2	MCF-7	breast:
5	chr14:68705377..68708933-chr14:69277914..69280943,3	MCF-7	breast:
6	chr14:69276177..69278251-chr20:45985801..45987904,2	MCF-7	breast:
7	chr14:69273277..69275385-chr14:69276944..69279019,2	K562	blood:
8	chr14:69270505..69278428-chr14:69279681..69285729,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000072121	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10139199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051533	0.87[GIH][hapmap]
rs11851414	0.87[GIH][hapmap]
rs12147199	1.00[ASN][1000 genomes]
rs12147461	1.00[ASN][1000 genomes]
rs1274955	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898320	1.00[ASN][1000 genomes]
rs194713	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194732	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs194743	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194745	0.89[YRI][hapmap]
rs2164627	1.00[ASN][1000 genomes]
rs4899261	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4899262	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902649	1.00[ASN][1000 genomes]
rs4902652	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55885232	1.00[ASN][1000 genomes]
rs56020080	1.00[ASN][1000 genomes]
rs56119720	1.00[ASN][1000 genomes]
rs58638884	1.00[ASN][1000 genomes]
rs7149650	0.92[AFR][1000 genomes]
rs72731537	1.00[ASN][1000 genomes]
rs72731539	1.00[ASN][1000 genomes]
rs72731544	1.00[ASN][1000 genomes]
rs72731547	1.00[ASN][1000 genomes]
rs72731549	1.00[ASN][1000 genomes]
rs72731550	1.00[ASN][1000 genomes]
rs72731551	1.00[ASN][1000 genomes]
rs72731554	1.00[ASN][1000 genomes]
rs72731565	1.00[ASN][1000 genomes]
rs72731567	1.00[ASN][1000 genomes]
rs72731576	1.00[ASN][1000 genomes]
rs72731577	1.00[ASN][1000 genomes]
rs72731579	1.00[ASN][1000 genomes]
rs72731581	1.00[ASN][1000 genomes]
rs73279198	0.92[AFR][1000 genomes]
rs8019383	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9671648	0.86[AFR][1000 genomes]
rs971290	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035267	chr14:69230254-69348126	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv542123	chr14:69230254-69348126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv902070	chr14:69244214-69308182	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Celiac disease	20190752	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4899260	Hs.304334	cis	multi-tissue	Pritchard
rs4899260	SMOC1	cis	cerebellum	SCAN
rs4899260	KIAA0247	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69264400-69281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr14:69271600-69281200	Enhancers	Fetal Muscle Leg	muscle
3	chr14:69271600-69281200	Enhancers	Fetal Stomach	stomach
4	chr14:69272400-69278600	Enhancers	Fetal Muscle Trunk	muscle
5	chr14:69272400-69279200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr14:69274000-69278400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr14:69274000-69278400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr14:69274000-69278800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr14:69274000-69281000	Weak transcription	Aorta	Aorta
10	chr14:69274000-69281000	Weak transcription	Fetal Brain Male	brain
11	chr14:69274200-69278800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:69274200-69279000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr14:69274200-69279200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr14:69274200-69279400	Weak transcription	GM12878-XiMat	blood
15	chr14:69274200-69279600	Weak transcription	Thymus	Thymus
16	chr14:69274200-69280000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:69274200-69280000	Weak transcription	Brain Substantia Nigra	brain
18	chr14:69274200-69280000	Weak transcription	Psoas Muscle	Psoas
19	chr14:69274200-69280800	Enhancers	Primary B cells from peripheral blood	blood
20	chr14:69274200-69281000	Weak transcription	Brain Angular Gyrus	brain
21	chr14:69274400-69279400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:69274400-69279600	Weak transcription	Brain Anterior Caudate	brain
23	chr14:69274400-69280800	Weak transcription	K562	blood
24	chr14:69274400-69281000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:69274400-69281000	Weak transcription	Osteobl	bone
26	chr14:69274600-69278800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:69274600-69279000	Weak transcription	Primary T cells from cord blood	blood
28	chr14:69274600-69280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:69274600-69280000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr14:69274600-69280400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:69274600-69280400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:69274600-69280400	Weak transcription	NHDF-Ad	bronchial
33	chr14:69274800-69278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr14:69274800-69280000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr14:69274800-69280000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr14:69274800-69280000	Weak transcription	HepG2	liver
37	chr14:69274800-69280200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr14:69274800-69280800	Weak transcription	HSMM	muscle
39	chr14:69275000-69279200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:69275000-69279200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:69275000-69280000	Weak transcription	Left Ventricle	heart
42	chr14:69275200-69279800	Weak transcription	Small Intestine	intestine
43	chr14:69275200-69280000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr14:69275200-69280000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:69275200-69280000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:69275400-69279800	Weak transcription	Liver	Liver
47	chr14:69275600-69279400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr14:69275600-69279800	Weak transcription	Colonic Mucosa	Colon
49	chr14:69275600-69280200	Weak transcription	HSMMtube	muscle
50	chr14:69275800-69279200	Weak transcription	Fetal Thymus	thymus

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