Variant report

Variant	rs11939690
Chromosome Location	chr4:159090555-159090556
allele	A/G
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	chr4:159090527-159090573	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159071408..159073828-chr4:159088522..159091495,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248429	TF binding region
FAM198B	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10021199	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs10517685	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10517686	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11100152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11933839	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17036992	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17036995	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17037201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17212066	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17212714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17271385	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17279270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725492	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2881374	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4234916	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4508943	1.00[CHB][hapmap]
rs4510503	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4549446	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6536289	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6536290	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6820988	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6834839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72691615	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691620	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691622	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691626	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691627	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691629	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691631	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691632	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691633	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691634	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691636	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72695726	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72695736	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72695741	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695744	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695745	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695747	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695748	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695750	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695751	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695753	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7678302	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997618	0.90[CEU][hapmap];1.00[CHB][hapmap]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11939690	FAM198B	cis	Whole Blood	GTEx
rs11939690	TMEM144	cis	Esophagus Muscularis	GTEx
rs11939690	RP11-597D13.9	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:159083000-159091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:159084200-159090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:159085000-159095200	Active TSS	Aorta	Aorta
5	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr4:159085400-159090800	Active TSS	Stomach Smooth Muscle	stomach
7	chr4:159085400-159095000	Active TSS	Right Atrium	heart
8	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr4:159086000-159090800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:159086200-159090600	Weak transcription	NH-A	brain
11	chr4:159086200-159091400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:159086400-159093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:159087400-159091000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:159087600-159091800	Active TSS	Ovary	ovary
15	chr4:159087800-159090600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:159087800-159090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:159088000-159091000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr4:159088400-159091600	Active TSS	Rectal Smooth Muscle	rectum
19	chr4:159088400-159094400	Active TSS	Right Ventricle	heart
20	chr4:159088600-159090600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:159088600-159092000	Active TSS	Brain Hippocampus Middle	brain
22	chr4:159088600-159094400	Active TSS	Fetal Heart	heart
23	chr4:159089000-159092000	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr4:159089000-159092600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:159089000-159092600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:159089000-159094600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:159089200-159090800	Enhancers	Brain Substantia Nigra	brain
28	chr4:159089200-159091600	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr4:159089200-159091600	Active TSS	NHDF-Ad	bronchial
30	chr4:159089200-159094200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:159089400-159090800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:159089600-159091000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr4:159089600-159092200	Active TSS	Duodenum Mucosa	Duodenum
34	chr4:159089600-159094000	Active TSS	Colon Smooth Muscle	Colon
35	chr4:159089600-159094200	Active TSS	Colonic Mucosa	Colon
36	chr4:159089800-159090600	Active TSS	Fetal Kidney	kidney
37	chr4:159089800-159090600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
38	chr4:159089800-159091000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:159089800-159091000	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr4:159089800-159091400	Active TSS	Brain Angular Gyrus	brain
41	chr4:159089800-159091600	Active TSS	Fetal Muscle Trunk	muscle
42	chr4:159089800-159091600	Active TSS	Placenta	Placenta
43	chr4:159089800-159091600	Active TSS	NHLF	lung
44	chr4:159089800-159093800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:159089800-159094600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:159090000-159090600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:159090000-159090600	Active TSS	Brain Cingulate Gyrus	brain
48	chr4:159090000-159091200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:159090000-159091400	Weak transcription	Small Intestine	intestine
50	chr4:159090000-159093800	Active TSS	Brain Anterior Caudate	brain

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