Variant report

Variant	rs17365723
Chromosome Location	chr1:84969019-84969020
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	chr1:84969014-84969029	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
3	MAFF	chr1:84968969-84969181	HepG2	liver:	n/a	chr1:84969110-84969128
4	POLR2A	chr1:84968320-84972670	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:84968524-84972839	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:84968683-84972955	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:84968805-84973213	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
2	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
SPATA1	TF binding region
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1395418	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17112247	0.84[CEU][hapmap]
rs17365681	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17374048	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs17374753	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17540101	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs312403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41284589	0.96[EUR][1000 genomes]
rs41284591	1.00[EUR][1000 genomes]
rs41284599	0.88[EUR][1000 genomes]
rs41293029	1.00[EUR][1000 genomes]
rs41302796	1.00[EUR][1000 genomes]
rs4512665	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4907081	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs72946368	0.94[EUR][1000 genomes]
rs72946369	0.96[EUR][1000 genomes]
rs72946390	0.96[EUR][1000 genomes]
rs72948408	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72948421	0.96[EUR][1000 genomes]
rs72948483	1.00[EUR][1000 genomes]
rs9432839	0.81[CEU][hapmap];0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
2	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
5	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:84954800-84969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:84956000-84969400	Weak transcription	Pancreas	Pancrea
8	chr1:84956800-84969400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:84956800-84970400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:84958600-84969400	Weak transcription	Gastric	stomach
11	chr1:84958600-84970400	Weak transcription	Lung	lung
12	chr1:84963000-84969400	Weak transcription	Spleen	Spleen
13	chr1:84963000-84969600	Weak transcription	Colonic Mucosa	Colon
14	chr1:84963800-84969400	Weak transcription	A549	lung
15	chr1:84963800-84970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:84963800-84970200	Weak transcription	Fetal Brain Male	brain
17	chr1:84963800-84970400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:84964000-84969400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:84964000-84969800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:84964000-84969800	Weak transcription	Ovary	ovary
21	chr1:84964000-84970200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:84964600-84969600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:84964800-84969400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:84964800-84969400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:84965800-84970400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:84966000-84969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:84966000-84969600	Weak transcription	Thymus	Thymus
28	chr1:84966400-84969200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
29	chr1:84966800-84970400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:84967000-84969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:84967000-84969400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:84967000-84969600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:84967000-84970000	Weak transcription	Placenta	Placenta
34	chr1:84967200-84969400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:84967400-84969400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:84967400-84969400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:84967400-84969600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:84967400-84970200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:84967400-84970600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:84967600-84969200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:84967600-84969400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:84967600-84969400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:84967600-84970600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:84967800-84970600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:84968000-84969200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:84968000-84969200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:84968000-84969400	Enhancers	Liver	Liver
48	chr1:84968000-84969600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:84968200-84969200	Weak transcription	Fetal Thymus	thymus
50	chr1:84968200-84969200	Enhancers	Rectal Mucosa Donor 31	rectum

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