Variant report

Variant	rs4240342
Chromosome Location	chr4:148795508-148795509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10013038	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10022144	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1036441	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519918	1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723235	0.84[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13147854	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17023771	1.00[CHD][hapmap]
rs17023933	0.86[ASN][1000 genomes]
rs17023942	0.86[ASN][1000 genomes]
rs17023992	1.00[ASN][1000 genomes]
rs2118034	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857095	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4240340	1.00[EUR][1000 genomes]
rs4835102	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835104	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4835105	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4835462	1.00[EUR][1000 genomes]
rs4835465	0.86[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835467	1.00[ASW][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535564	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535566	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851336	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6852320	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6853610	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6856071	1.00[YRI][hapmap]
rs72955571	1.00[EUR][1000 genomes]
rs7435763	1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654818	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661267	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687859	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700162	1.00[EUR][1000 genomes]
rs893030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4240342	FAM118A	trans	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148763200-148796200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:148766600-148796200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:148767600-148796400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:148768400-148815600	Weak transcription	Primary T cells from cord blood	blood
5	chr4:148770400-148796200	Weak transcription	Fetal Kidney	kidney
6	chr4:148772000-148806000	Weak transcription	Fetal Thymus	thymus
7	chr4:148777000-148796200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:148777000-148823000	Weak transcription	Small Intestine	intestine
9	chr4:148777400-148796600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:148777800-148796200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:148782000-148799400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:148783000-148796200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:148783000-148796200	Weak transcription	Thymus	Thymus
14	chr4:148783400-148796400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:148783400-148796400	Weak transcription	Lung	lung
16	chr4:148783600-148796200	Weak transcription	Esophagus	oesophagus
17	chr4:148783600-148796200	Weak transcription	Placenta	Placenta
18	chr4:148783800-148796200	Weak transcription	Fetal Intestine Large	intestine
19	chr4:148783800-148796200	Weak transcription	Gastric	stomach
20	chr4:148783800-148796200	Weak transcription	Right Ventricle	heart
21	chr4:148784400-148810800	Weak transcription	Fetal Heart	heart
22	chr4:148784600-148796400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:148785400-148796200	Weak transcription	GM12878-XiMat	blood
24	chr4:148785600-148796200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:148786000-148804000	Weak transcription	Psoas Muscle	Psoas
26	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
27	chr4:148786400-148796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:148787400-148795600	Weak transcription	NH-A	brain
29	chr4:148787400-148796200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:148787400-148800400	Weak transcription	NHEK	skin
31	chr4:148787600-148796200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:148787600-148796200	Weak transcription	Osteobl	bone
33	chr4:148787600-148801600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:148788000-148796200	Weak transcription	HUVEC	blood vessel
35	chr4:148788000-148798400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:148788000-148800200	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:148788400-148796200	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:148788600-148796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:148788600-148796200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:148788600-148796600	Weak transcription	HMEC	breast
41	chr4:148788600-148796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:148788800-148796200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:148788800-148796400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:148788800-148803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:148789800-148805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:148790200-148796200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:148790200-148796200	Weak transcription	Left Ventricle	heart
48	chr4:148790200-148796200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:148790200-148799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:148790400-148796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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