Variant report

Variant	rs2438140
Chromosome Location	chr4:95407821-95407822
allele	C/T
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	POLR2A	chr4:95407732-95407983	HUVEC	blood vessel:	n/a	n/a
2	MYC	chr4:95407646-95407941	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:95407536-95407954	MCF10A-Er-Src	breast:	n/a	chr4:95407789-95407798
4	POLR2A	chr4:95407809-95407837	HUVEC	blood vessel:	n/a	n/a
5	STAT3	chr4:95407539-95407986	MCF10A-Er-Src	breast:	n/a	chr4:95407803-95407814 chr4:95407799-95407819 chr4:95407805-95407813
6	POLR2A	chr4:95407458-95408151	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:95407519-95408144	HUVEC	blood vessel:	n/a	n/a
8	FOS	chr4:95407705-95407861	MCF10A-Er-Src	breast:	n/a	chr4:95407789-95407798
9	STAT3	chr4:95407380-95408014	MCF10A-Er-Src	breast:	n/a	chr4:95407803-95407814 chr4:95407799-95407819 chr4:95407805-95407813
10	FOS	chr4:95407493-95407942	MCF10A-Er-Src	breast:	n/a	chr4:95407789-95407798
11	STAT3	chr4:95407504-95407982	MCF10A-Er-Src	breast:	n/a	chr4:95407803-95407814 chr4:95407799-95407819 chr4:95407805-95407813
12	TCF12	chr4:95407533-95408061	SK-N-SH	brain:	n/a	n/a
13	GATA2	chr4:95407617-95408060	HUVEC	blood vessel:	n/a	n/a
14	MYC	chr4:95407734-95407845	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr4:95407593-95407851	MCF10A-Er-Src	breast:	n/a	chr4:95407803-95407814 chr4:95407799-95407819 chr4:95407805-95407813
16	FOS	chr4:95407664-95407828	MCF10A-Er-Src	breast:	n/a	chr4:95407789-95407798

No.	Distal block	Cell Line	Cell type
1	chr4:95380389..95383633-chr4:95406287..95409209,3	K562	blood:
2	chr4:95405668..95407822-chr7:100027413..100029654,2	K562	blood:
3	chr4:95406401..95409166-chr4:95410541..95413681,3	K562	blood:
4	chr4:95406132..95409041-chr4:95429869..95431483,2	K562	blood:
5	chr4:95397926..95400285-chr4:95407452..95409108,2	K562	blood:
6	chr4:95395769..95400285-chr4:95406149..95409946,5	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1082513	0.82[ASN][1000 genomes]
rs1493109	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493111	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17378777	0.82[MEX][hapmap]
rs1845176	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2433320	0.80[MEX][hapmap]
rs2433322	0.82[MEX][hapmap]
rs2433327	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2438146	0.86[MEX][hapmap]
rs2452010	0.86[MEX][hapmap]
rs2452555	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452563	0.84[CHB][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2452567	0.81[ASN][1000 genomes]
rs2510764	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2510777	0.82[MEX][hapmap]
rs2510781	0.86[MEX][hapmap]
rs2510793	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2510796	0.82[ASN][1000 genomes]
rs2510797	0.83[ASN][1000 genomes]
rs2555215	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639794	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7697295	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs774982	0.84[CEU][hapmap]
rs774984	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774985	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs774987	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs774990	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs774991	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9990976	0.91[ASW][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][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	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2438140	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95387400-95410000	Weak transcription	NHLF	lung
3	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:95396800-95410000	Weak transcription	Fetal Intestine Large	intestine
8	chr4:95398400-95408800	Weak transcription	Brain Substantia Nigra	brain
9	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
10	chr4:95399000-95409800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:95400800-95440000	Weak transcription	Lung	lung
13	chr4:95401800-95408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:95402000-95408600	Weak transcription	Right Atrium	heart
16	chr4:95402000-95409000	Weak transcription	NHDF-Ad	bronchial
17	chr4:95402000-95409200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:95402000-95409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
20	chr4:95402200-95412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:95402200-95412200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:95402200-95412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
24	chr4:95403800-95417800	Weak transcription	HepG2	liver
25	chr4:95404000-95408600	Weak transcription	Ovary	ovary
26	chr4:95404000-95409800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
28	chr4:95404400-95412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:95405000-95408000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:95405000-95408800	Weak transcription	Liver	Liver
31	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:95405400-95409000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:95405800-95408000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:95405800-95408000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:95405800-95408000	Enhancers	Hela-S3	cervix
36	chr4:95405800-95409800	Genic enhancers	Osteobl	bone
37	chr4:95406000-95410200	Enhancers	HMEC	breast
38	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
39	chr4:95406200-95408400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:95406200-95408600	Enhancers	HUVEC	blood vessel
41	chr4:95406200-95410600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:95406400-95408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:95406400-95408000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:95406400-95408200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:95406400-95408600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:95406400-95409000	Genic enhancers	NHEK	skin
47	chr4:95406400-95409200	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:95406400-95410000	Weak transcription	HSMMtube	muscle
49	chr4:95406400-95411800	Weak transcription	HSMM	muscle
50	chr4:95406600-95409800	Weak transcription	Rectal Smooth Muscle	rectum

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