Variant report

Variant	rs17490973
Chromosome Location	chr3:111601158-111601159
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	chr3:111601153-111601344	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:111601086-111601814	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:111601055-111601288	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111599284..111601427-chr3:111601779..111604695,2	K562	blood:

Variant related genes	Relation type
PHLDB2	TF binding region
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1443078	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs17424897	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs17429033	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs17490485	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17491120	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34431304	0.80[EUR][1000 genomes]
rs57821301	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73852716	0.84[AMR][1000 genomes]
rs73852719	0.84[AMR][1000 genomes]
rs73852723	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv980070	chr3:111592547-111602240	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17490973	CXCL11	trans	brain	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
3	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
4	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
5	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
6	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:111589800-111603400	Weak transcription	Pancreas	Pancrea
8	chr3:111591600-111603200	Weak transcription	Ovary	ovary
9	chr3:111591600-111603600	Weak transcription	HepG2	liver
10	chr3:111591600-111610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:111591600-111633200	Weak transcription	Fetal Kidney	kidney
12	chr3:111593400-111601400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:111593600-111601400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:111593600-111603000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:111593600-111603000	Weak transcription	Lung	lung
16	chr3:111593600-111603200	Weak transcription	Gastric	stomach
17	chr3:111593600-111603400	Weak transcription	HSMM	muscle
18	chr3:111593600-111608800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:111593800-111601200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:111593800-111602000	Weak transcription	HUVEC	blood vessel
21	chr3:111593800-111602800	Weak transcription	NHLF	lung
22	chr3:111593800-111603000	Weak transcription	Fetal Stomach	stomach
23	chr3:111593800-111603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:111593800-111603400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:111594000-111603400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:111594400-111603200	Weak transcription	HMEC	breast
27	chr3:111595200-111601200	Weak transcription	NHEK	skin
28	chr3:111595400-111601200	Weak transcription	Osteobl	bone
29	chr3:111595400-111602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:111598400-111612600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:111599200-111603400	Weak transcription	Right Atrium	heart
32	chr3:111599400-111603600	Weak transcription	NH-A	brain
33	chr3:111599600-111601200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:111599600-111602400	Weak transcription	Hela-S3	cervix
35	chr3:111599600-111603000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:111599600-111603000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:111600200-111601200	Weak transcription	Left Ventricle	heart
38	chr3:111600200-111602800	Weak transcription	Liver	Liver
39	chr3:111600200-111603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:111600200-111603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:111600200-111604000	Weak transcription	A549	lung
42	chr3:111600400-111602000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:111600400-111602600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:111600400-111603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:111600400-111603400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:111600400-111603600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:111600600-111603000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:111600600-111603000	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:111600600-111603200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:111600600-111603200	Weak transcription	Fetal Intestine Small	intestine

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