Variant report

Variant	rs1464361
Chromosome Location	chr3:101073550-101073551
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	chr3:101073363-101073584	K562	blood:	n/a	n/a

Variant related genes	Relation type
ZNF90P1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1078153	0.89[EUR][1000 genomes]
rs11929578	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12491044	0.88[EUR][1000 genomes]
rs1426386	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1569071	0.89[EUR][1000 genomes]
rs2176887	0.84[EUR][1000 genomes]
rs2433032	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2449824	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2460721	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2553414	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2553420	0.89[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2553421	0.82[EUR][1000 genomes]
rs2553422	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2553423	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2553428	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2682387	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682389	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3846092	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4234491	0.89[EUR][1000 genomes]
rs4683930	0.88[EUR][1000 genomes]
rs472751	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs485037	0.89[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs485793	0.89[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503252	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503669	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs504482	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs513283	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs524261	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs534119	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs535779	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs551395	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs554030	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs556820	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs565914	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs566292	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61379928	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs63482	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6768114	0.88[EUR][1000 genomes]
rs6779775	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6788864	0.89[EUR][1000 genomes]
rs6791803	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6809436	1.00[CEU][hapmap]
rs72942230	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72942264	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72948053	0.88[EUR][1000 genomes]
rs7618600	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621062	0.89[EUR][1000 genomes]
rs7638284	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648141	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs770968	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9917699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:101038600-101101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:101038800-101089800	Weak transcription	Pancreas	Pancrea
4	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
5	chr3:101040600-101086800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:101040800-101076000	Weak transcription	Esophagus	oesophagus
7	chr3:101040800-101090000	Weak transcription	Brain Angular Gyrus	brain
8	chr3:101042800-101089600	Weak transcription	NH-A	brain
9	chr3:101043200-101076000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:101043200-101105000	Weak transcription	Brain Anterior Caudate	brain
11	chr3:101043800-101096600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:101044400-101074200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:101044400-101103000	Weak transcription	Gastric	stomach
14	chr3:101044600-101076000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:101044600-101081800	Weak transcription	Aorta	Aorta
16	chr3:101044800-101079800	Weak transcription	Spleen	Spleen
17	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:101046400-101074200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:101046400-101076200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:101046400-101089000	Weak transcription	Fetal Brain Male	brain
21	chr3:101046800-101074200	Weak transcription	Fetal Brain Female	brain
22	chr3:101046800-101076000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:101046800-101076200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:101047200-101076200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:101047400-101096000	Weak transcription	Psoas Muscle	Psoas
26	chr3:101048400-101075800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:101048400-101076600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:101048400-101082400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:101048400-101084400	Weak transcription	HSMM	muscle
30	chr3:101048600-101088000	Weak transcription	HUVEC	blood vessel
31	chr3:101049200-101096000	Weak transcription	Ovary	ovary
32	chr3:101049200-101102200	Weak transcription	Right Ventricle	heart
33	chr3:101050400-101074400	Weak transcription	Left Ventricle	heart
34	chr3:101053200-101082600	Weak transcription	Fetal Stomach	stomach
35	chr3:101053200-101083200	Weak transcription	K562	blood
36	chr3:101054600-101085000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:101055800-101076000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:101056200-101076000	Weak transcription	Lung	lung
39	chr3:101056200-101081600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:101056200-101082600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:101056200-101082800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:101056200-101084600	Weak transcription	Fetal Heart	heart
43	chr3:101058200-101081800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:101059800-101082800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:101060000-101074400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:101061600-101076000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:101062200-101075800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:101062600-101079200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:101062800-101074600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:101062800-101076000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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