Variant report

Variant	rs17880982
Chromosome Location	chr4:74120167-74120168
allele	A/C
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	chr4:74120042-74120251	K562	blood:	n/a	n/a
2	POLR2A	chr4:74120125-74120268	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:73932268..73935243-chr4:74118599..74120212,2	K562	blood:
2	chr4:73944396..73945924-chr4:74118345..74120655,2	K562	blood:

Variant related genes	Relation type
ENSG00000250220	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10092	0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs12512671	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs13119179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs13133680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap]
rs16849364	1.00[ASW][hapmap];0.87[MKK][hapmap]
rs2137445	1.00[LWK][hapmap]
rs2306058	1.00[ASW][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap]
rs2306059	1.00[LWK][hapmap]
rs2366792	0.83[CHB][hapmap]
rs66550905	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7664273	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][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	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000509	chr4:73968978-74206949	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv3410570	chr4:74055180-74122498	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17880982	SMR3B	cis	parietal	SCAN
rs17880982	ANKRD56	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74056000-74123000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:74059600-74123000	Weak transcription	Esophagus	oesophagus
3	chr4:74078200-74123000	Weak transcription	Lung	lung
4	chr4:74087800-74123400	Weak transcription	Gastric	stomach
5	chr4:74089000-74121400	Weak transcription	Hela-S3	cervix
6	chr4:74089200-74122000	Weak transcription	Aorta	Aorta
7	chr4:74089400-74121800	Weak transcription	NHLF	lung
8	chr4:74099800-74122400	Weak transcription	Stomach Mucosa	stomach
9	chr4:74101000-74121200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:74101000-74122000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:74101000-74122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:74101000-74122600	Weak transcription	Fetal Stomach	stomach
13	chr4:74101000-74123000	Weak transcription	Placenta	Placenta
14	chr4:74101200-74122400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:74101400-74121200	Weak transcription	NHEK	skin
16	chr4:74101400-74121800	Weak transcription	Fetal Kidney	kidney
17	chr4:74102200-74122400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:74103200-74120400	Weak transcription	Brain Germinal Matrix	brain
19	chr4:74104600-74121200	Weak transcription	A549	lung
20	chr4:74106600-74123000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:74109000-74121200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:74111200-74121200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:74111200-74122400	Weak transcription	Ovary	ovary
24	chr4:74111400-74121800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:74111400-74121800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:74111400-74122000	Weak transcription	HSMMtube	muscle
27	chr4:74111400-74122400	Weak transcription	Colonic Mucosa	Colon
28	chr4:74111400-74122800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:74111400-74123000	Weak transcription	Pancreas	Pancrea
30	chr4:74111800-74121200	Weak transcription	Primary B cells from cord blood	blood
31	chr4:74111800-74121600	Weak transcription	Right Ventricle	heart
32	chr4:74112000-74121600	Weak transcription	Thymus	Thymus
33	chr4:74112400-74120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:74112400-74121000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:74112400-74121200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:74112400-74121200	Weak transcription	Psoas Muscle	Psoas
37	chr4:74112400-74121600	Weak transcription	Fetal Intestine Large	intestine
38	chr4:74112400-74121800	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:74112400-74122400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:74112400-74123200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:74114600-74120400	Strong transcription	Fetal Thymus	thymus
42	chr4:74114600-74120600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:74115600-74120800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:74115600-74122000	Weak transcription	Right Atrium	heart
45	chr4:74116000-74121800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:74116400-74123400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:74116600-74120800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:74116600-74121000	Genic enhancers	Dnd41	blood
49	chr4:74116800-74121800	Weak transcription	Fetal Intestine Small	intestine
50	chr4:74116800-74122600	Weak transcription	Fetal Muscle Leg	muscle

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