Variant report

Variant	rs55678532
Chromosome Location	chr1:172524552-172524553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172417892..172422705-chr1:172522786..172525518,5	MCF-7	breast:
2	chr1:172500340..172502764-chr1:172523653..172526492,2	K562	blood:
3	chr1:172518787..172521238-chr1:172523963..172525755,2	MCF-7	breast:
4	chr1:172518503..172521143-chr1:172524413..172526637,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs2472551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2516063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35344763	1.00[EUR][1000 genomes]
rs56001419	1.00[EUR][1000 genomes]
rs56884575	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57117081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57600271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58097538	1.00[EUR][1000 genomes]
rs58481917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58852323	1.00[EUR][1000 genomes]
rs58899638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60296720	1.00[EUR][1000 genomes]
rs60345777	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60485575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61692965	1.00[EUR][1000 genomes]
rs6683359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73032190	1.00[EUR][1000 genomes]
rs73034011	1.00[EUR][1000 genomes]
rs74124226	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74124231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124236	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124248	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124250	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124251	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124253	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124256	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124257	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124258	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74124263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7526530	1.00[EUR][1000 genomes]
rs7538218	1.00[EUR][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	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv872548	chr1:172518012-172551724	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
2	chr1:172503400-172528600	Weak transcription	Lung	lung
3	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
4	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:172504200-172527000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172506200-172525000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:172506200-172526200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
11	chr1:172507400-172526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:172508200-172526400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:172510000-172525000	Weak transcription	Left Ventricle	heart
16	chr1:172511800-172524800	Weak transcription	Liver	Liver
17	chr1:172511800-172528600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:172512000-172529000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:172512000-172534200	Weak transcription	Gastric	stomach
21	chr1:172513600-172524600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:172513800-172525000	Weak transcription	Fetal Thymus	thymus
23	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
24	chr1:172514400-172526200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:172514800-172528600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:172514800-172530200	Weak transcription	Thymus	Thymus
27	chr1:172515200-172524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:172515200-172525200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:172515200-172528000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:172515200-172528200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:172515400-172528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:172516000-172532800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:172516200-172528800	Weak transcription	Pancreas	Pancrea
34	chr1:172516400-172526400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:172516400-172527400	Weak transcription	NHLF	lung
36	chr1:172516600-172528800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
38	chr1:172517800-172527200	Weak transcription	Fetal Kidney	kidney
39	chr1:172518000-172529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:172518600-172533000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:172518800-172525000	Weak transcription	HepG2	liver
42	chr1:172519000-172525600	Weak transcription	Fetal Brain Female	brain
43	chr1:172519000-172530000	Weak transcription	NH-A	brain
44	chr1:172519000-172530200	Weak transcription	Brain Substantia Nigra	brain
45	chr1:172519200-172526800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:172519200-172526800	Weak transcription	A549	lung
47	chr1:172519200-172527200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:172519200-172528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:172519200-172529000	Weak transcription	Brain Germinal Matrix	brain
50	chr1:172519200-172534600	Weak transcription	Right Ventricle	heart

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