Variant report

Variant	rs4873102
Chromosome Location	chr8:48352405-48352406
allele	A/G
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	EP300	chr8:48351969-48352566	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr8:48351935-48352608	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr8:48352054-48352598	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr8:48352055-48352657	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
SPIDR	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10086987	0.80[EUR][1000 genomes]
rs10102598	0.80[EUR][1000 genomes]
rs1038797	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808752	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10957074	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10958058	0.95[JPT][hapmap]
rs1106607	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs11774001	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11775514	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11775628	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11779308	0.81[EUR][1000 genomes]
rs11779423	0.82[EUR][1000 genomes]
rs11781727	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11782572	0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs11783141	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11784823	1.00[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap]
rs11785228	0.98[EUR][1000 genomes]
rs12541086	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs12543823	0.95[EUR][1000 genomes]
rs12544329	0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap]
rs12547513	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12549996	0.95[JPT][hapmap]
rs12550067	0.80[EUR][1000 genomes]
rs12680669	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12682269	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13259872	0.82[EUR][1000 genomes]
rs13259913	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2087656	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2130413	1.00[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap]
rs2130879	0.93[EUR][1000 genomes]
rs2172121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2362554	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs34099416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs35045730	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35235599	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4242439	0.82[EUR][1000 genomes]
rs4388466	0.82[EUR][1000 genomes]
rs4495437	0.80[EUR][1000 genomes]
rs4498545	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4608108	0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4872957	0.82[EUR][1000 genomes]
rs4873106	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4873293	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4873395	1.00[ASW][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap]
rs4873437	0.95[JPT][hapmap]
rs6472229	0.92[EUR][1000 genomes]
rs6981790	0.94[EUR][1000 genomes]
rs6982620	0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs6990123	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6994218	0.94[EUR][1000 genomes]
rs7012341	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7819806	0.82[EUR][1000 genomes]
rs7826284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7839134	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs902619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4873102	KIAA0146	cis	parietal	SCAN
rs4873102	MCM4	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48310800-48354800	Weak transcription	Right Ventricle	heart
2	chr8:48311600-48353000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr8:48312200-48353000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:48312800-48358600	Weak transcription	Thymus	Thymus
5	chr8:48312800-48367600	Weak transcription	Pancreas	Pancrea
6	chr8:48312800-48377000	Weak transcription	Esophagus	oesophagus
7	chr8:48313200-48361000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr8:48313400-48352800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:48323000-48354200	Weak transcription	Spleen	Spleen
10	chr8:48323000-48364400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:48326000-48366000	Weak transcription	Gastric	stomach
12	chr8:48326200-48354800	Weak transcription	HMEC	breast
13	chr8:48326200-48362600	Weak transcription	Colon Smooth Muscle	Colon
14	chr8:48328400-48362600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr8:48328600-48352600	Weak transcription	Dnd41	blood
16	chr8:48328600-48361800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:48328600-48362400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr8:48328600-48364000	Weak transcription	Fetal Intestine Large	intestine
19	chr8:48328600-48371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr8:48328600-48374600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:48334600-48352800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr8:48335000-48362400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr8:48335400-48363400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:48337800-48357000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr8:48340200-48356800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:48340400-48364000	Weak transcription	Lung	lung
27	chr8:48340600-48365600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:48342000-48353000	Weak transcription	Right Atrium	heart
29	chr8:48342000-48362600	Weak transcription	Ovary	ovary
30	chr8:48342200-48372600	Weak transcription	Liver	Liver
31	chr8:48342600-48364000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr8:48342800-48355600	Weak transcription	Fetal Brain Female	brain
33	chr8:48343000-48354800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr8:48343800-48366800	Weak transcription	Aorta	Aorta
35	chr8:48343800-48371400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr8:48344000-48352600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:48344200-48355000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:48344200-48355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr8:48344200-48363200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr8:48344400-48353000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr8:48344400-48363200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr8:48344800-48362800	Weak transcription	A549	lung
43	chr8:48345000-48369800	Weak transcription	NH-A	brain
44	chr8:48345000-48370600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:48346200-48362600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:48346800-48358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:48347200-48366000	Weak transcription	Fetal Thymus	thymus
48	chr8:48348800-48355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:48349600-48362400	Weak transcription	Fetal Intestine Small	intestine
50	chr8:48349600-48363800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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