Variant report

Variant	rs774984
Chromosome Location	chr4:95409567-95409568
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	chr4:95408960-95411285	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:95408889-95411285	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr4:95409558-95409750	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95372926..95375393-chr4:95409110..95411441,2	MCF-7	breast:
2	chr4:95395769..95400285-chr4:95406149..95409946,5	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1082513	0.82[ASN][1000 genomes]
rs12639887	0.87[ASW][hapmap]
rs1493109	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.94[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	0.81[MEX][hapmap]
rs2433322	0.82[MEX][hapmap]
rs2433327	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2438140	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]
rs2438146	0.86[MEX][hapmap]
rs2452010	0.86[MEX][hapmap]
rs2452555	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452563	0.85[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2452567	0.81[ASN][1000 genomes]
rs2510764	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[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];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639794	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7697295	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs774982	0.88[CEU][hapmap]
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	0.80[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[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
rs774984	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:64 , 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	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
9	chr4:95399000-95409800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:95400800-95440000	Weak transcription	Lung	lung
12	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:95402000-95409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
15	chr4:95402200-95412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:95402200-95412200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:95402200-95412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
19	chr4:95403800-95417800	Weak transcription	HepG2	liver
20	chr4:95404000-95409800	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
22	chr4:95404400-95412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:95405800-95409800	Genic enhancers	Osteobl	bone
25	chr4:95406000-95410200	Enhancers	HMEC	breast
26	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
27	chr4:95406200-95410600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:95406400-95410000	Weak transcription	HSMMtube	muscle
29	chr4:95406400-95411800	Weak transcription	HSMM	muscle
30	chr4:95406600-95409800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:95406800-95409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:95407200-95410600	Enhancers	Fetal Heart	heart
33	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
34	chr4:95407600-95410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:95407800-95409800	Enhancers	A549	lung
36	chr4:95408000-95409600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:95408000-95409800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:95408000-95410000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:95408000-95410400	Enhancers	Psoas Muscle	Psoas
40	chr4:95408000-95412200	Weak transcription	Right Ventricle	heart
41	chr4:95408000-95412600	Weak transcription	Stomach Mucosa	stomach
42	chr4:95408000-95428000	Weak transcription	K562	blood
43	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:95408400-95410600	Enhancers	Hela-S3	cervix
45	chr4:95408600-95411000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:95408800-95410200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr4:95409000-95409600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr4:95409000-95409600	Enhancers	NHEK	skin
49	chr4:95409000-95409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:95409000-95410400	Enhancers	NH-A	brain

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