Variant report

Variant	rs2280099
Chromosome Location	chr4:90035549-90035550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr4:90034937-90035615	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:90032368-90036875	HepG2	liver:	n/a	n/a
3	TEAD4	chr4:90035087-90035615	HepG2	liver:	n/a	n/a
4	SPI1	chr4:90035429-90035611	GM12878	blood:	n/a	n/a
5	CUX1	chr4:90035075-90035583	GM12878	blood:	n/a	n/a
6	FOXA1	chr4:90035129-90035642	HepG2	liver:	n/a	n/a
7	BATF	chr4:90035288-90035559	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:90032629-90036890	K562	blood:	n/a	n/a
9	FOSL2	chr4:90035250-90035598	HepG2	liver:	n/a	n/a
10	MXI1	chr4:90034666-90035571	HepG2	liver:	n/a	n/a
11	MAFK	chr4:90035305-90035593	HepG2	liver:	n/a	n/a
12	SPI1	chr4:90035312-90035630	GM12878	blood:	n/a	n/a
13	MYBL2	chr4:90034482-90035658	HepG2	liver:	n/a	n/a
14	EBF1	chr4:90035418-90035569	GM12878	blood:	n/a	n/a
15	FOXA1	chr4:90035157-90035635	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:90031723-90036966	HepG2	liver:	n/a	n/a
17	BHLHE40	chr4:90035267-90035551	HepG2	liver:	n/a	n/a
18	FOXA1	chr4:90035185-90035601	HepG2	liver:	n/a	n/a
19	JUND	chr4:90035275-90035560	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90032004..90034943-chr4:90035415..90038647,4	MCF-7	breast:

No data

Variant related genes	Relation type
FAM13A	TF binding region
ENSG00000270720	TF binding region
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction
ENSG00000180346	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10025332	0.83[ASN][1000 genomes]
rs10516826	0.92[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10516828	1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12507349	0.89[ASN][1000 genomes]
rs1343921	0.88[JPT][hapmap]
rs1398945	0.89[ASN][1000 genomes]
rs1513820	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768752	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17769356	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17770293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17819929	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17820320	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17821105	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795731	0.93[GIH][hapmap]
rs1921680	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175821	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2670625	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs2869974	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3822085	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5026462	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55806245	0.84[ASN][1000 genomes]
rs55885459	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55987745	0.87[ASN][1000 genomes]
rs55996516	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56038841	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56111951	0.89[ASN][1000 genomes]
rs56147277	0.84[ASN][1000 genomes]
rs56165603	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344658	0.89[ASN][1000 genomes]
rs56355329	0.89[ASN][1000 genomes]
rs56672432	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56719325	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59188553	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59283403	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59586695	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60213126	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60591238	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60751124	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61082288	0.84[ASN][1000 genomes]
rs62306393	0.98[ASN][1000 genomes]
rs6822256	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6825767	0.83[ASN][1000 genomes]
rs6825804	0.83[ASN][1000 genomes]
rs6826703	0.81[ASN][1000 genomes]
rs6832298	0.84[ASN][1000 genomes]
rs72665855	0.81[ASN][1000 genomes]
rs72665867	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665868	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72665882	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665892	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665898	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665902	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72668111	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668112	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668120	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668125	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668127	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668130	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668134	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668135	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668138	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72668144	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668152	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668154	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668156	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668157	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668165	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668167	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668171	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668179	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668183	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668187	0.89[ASN][1000 genomes]
rs72668189	0.87[ASN][1000 genomes]
rs72668192	0.84[ASN][1000 genomes]
rs72668193	0.84[ASN][1000 genomes]
rs72668195	0.83[ASN][1000 genomes]
rs72668196	0.83[ASN][1000 genomes]
rs72670003	0.83[ASN][1000 genomes]
rs7440590	0.82[CHD][hapmap]
rs756227	0.83[ASN][1000 genomes]
rs7660709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7669140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7689498	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7691983	0.82[CHD][hapmap]
rs8582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993181	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280099	KLK7	trans	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90036400	Weak transcription	HUVEC	blood vessel
4	chr4:90033600-90038400	Weak transcription	Psoas Muscle	Psoas
5	chr4:90033600-90039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:90033600-90039000	Weak transcription	Lung	lung
7	chr4:90033600-90040800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
10	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
11	chr4:90033600-90049200	Weak transcription	Gastric	stomach
12	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
13	chr4:90033800-90036200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:90033800-90037600	Weak transcription	Fetal Thymus	thymus
15	chr4:90033800-90037600	Weak transcription	HSMM	muscle
16	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:90034000-90035600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:90034000-90036400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:90034000-90037000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:90034000-90037000	Weak transcription	Fetal Lung	lung
21	chr4:90034000-90038400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:90034000-90038800	Weak transcription	Fetal Kidney	kidney
23	chr4:90034000-90039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:90034000-90040400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:90034000-90040400	Weak transcription	NH-A	brain
26	chr4:90034000-90040800	Weak transcription	Osteobl	bone
27	chr4:90034000-90041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:90034200-90035800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:90034200-90038400	Weak transcription	Fetal Brain Male	brain
32	chr4:90034200-90040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:90034200-90040800	Weak transcription	NHDF-Ad	bronchial
34	chr4:90034200-90041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:90034400-90035600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:90034400-90036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:90034400-90039000	Weak transcription	Dnd41	blood
39	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
41	chr4:90034600-90035600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:90034600-90036200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:90034600-90037000	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr4:90034600-90040400	Weak transcription	HMEC	breast
45	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
46	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:90034800-90035600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:90034800-90035600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:90034800-90039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:90034800-90040400	Weak transcription	NHEK	skin

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