Variant report

Variant	rs11102678
Chromosome Location	chr1:114282287-114282288
allele	A/C
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	chr1:114282262-114282430	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114281940..114285839-chr1:114300217..114304020,4	K562	blood:

Variant related genes	Relation type
PHTF1	TF binding region
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10776773	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10858015	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102667	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1146183	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1146184	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1146185	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12138638	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12144309	0.83[GIH][hapmap]
rs1217225	0.81[ASW][hapmap]
rs1217375	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1217379	0.85[LWK][hapmap]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.90[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1217406	0.87[ASW][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap]
rs1217408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1217414	0.81[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap]
rs1217417	0.84[ASN][1000 genomes]
rs1217418	0.81[ASW][hapmap];0.90[LWK][hapmap]
rs1217419	0.87[ASW][hapmap];0.85[LWK][hapmap]
rs1230673	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1230681	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1230684	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1235000	0.81[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs13524	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1624335	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap]
rs1743594	0.94[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1746857	0.95[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2040041	0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2185827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2476599	1.00[ASW][hapmap];0.81[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2476600	0.85[LWK][hapmap]
rs2476602	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2636000	0.95[ASN][1000 genomes]
rs2636003	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2797416	0.85[LWK][hapmap]
rs3789597	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3789600	0.87[ASW][hapmap];0.83[LWK][hapmap]
rs6537798	0.87[ASW][hapmap]
rs7543121	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7555634	0.85[LWK][hapmap]
rs971173	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS 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	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11102678	AP4B1	cis	cerebellum	SCAN
rs11102678	RAP1A	cis	parietal	SCAN
rs11102678	PHTF1	cis	parietal	SCAN
rs11102678	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
2	chr1:114228000-114287800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
4	chr1:114242000-114300000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:114245600-114300600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:114248800-114290200	Weak transcription	HMEC	breast
7	chr1:114251000-114291400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:114256600-114283600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:114256600-114288800	Weak transcription	K562	blood
10	chr1:114257600-114283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:114257600-114296200	Weak transcription	Pancreas	Pancrea
12	chr1:114258000-114300000	Weak transcription	Right Ventricle	heart
13	chr1:114261400-114300000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:114261400-114300600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:114261400-114301000	Weak transcription	Lung	lung
16	chr1:114261600-114300200	Weak transcription	Brain Angular Gyrus	brain
17	chr1:114261600-114300600	Weak transcription	Aorta	Aorta
18	chr1:114261600-114300600	Weak transcription	Esophagus	oesophagus
19	chr1:114261600-114300600	Weak transcription	Gastric	stomach
20	chr1:114262000-114286400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:114263600-114285400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:114263600-114300000	Weak transcription	Fetal Lung	lung
23	chr1:114263600-114300400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:114264000-114300400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:114264200-114300000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:114264400-114288200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:114264800-114290200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:114265000-114283600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:114265000-114291200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:114265200-114283600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:114267200-114290000	Weak transcription	NHEK	skin
32	chr1:114267400-114299400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:114267400-114300000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:114268400-114292000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:114268400-114298000	Weak transcription	A549	lung
36	chr1:114268600-114292000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:114268600-114292600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:114268600-114296200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:114268800-114296400	Weak transcription	NHLF	lung
40	chr1:114268800-114299200	Weak transcription	Fetal Brain Female	brain
41	chr1:114269200-114296000	Weak transcription	Ovary	ovary
42	chr1:114271000-114287400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:114271200-114283000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:114272800-114300000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:114275200-114286600	Weak transcription	Brain Substantia Nigra	brain
46	chr1:114275200-114292600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:114276000-114285800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:114277800-114299200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:114278400-114283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:114279200-114282600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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