Variant report

Variant	rs2899827
Chromosome Location	chr15:75101127-75101128
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	chr15:75100811-75101258	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75101016-75101296	H1-neurons	neurons:	n/a	n/a
3	MTA3	chr15:75100747-75101263	GM12878	blood:	n/a	n/a
4	FOS	chr15:75100604-75101127	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr15:75101059-75101188	GM12878	blood:	n/a	n/a
6	RCOR1	chr15:75100417-75101438	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:75101052-75101136	ProgFib	skin:	n/a	n/a
8	GTF2F1	chr15:75101083-75101186	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75094936..75097374-chr15:75098181..75101253,3	K562	blood:
2	chr15:75080438..75082798-chr15:75099156..75102028,3	K562	blood:
3	chr15:75092440..75094935-chr15:75099537..75102010,2	MCF-7	breast:
4	chr15:75090435..75094394-chr15:75099172..75101373,3	K562	blood:

Variant related genes	Relation type
LMAN1L	TF binding region
ENSG00000264386	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12438333	1.00[CEU][hapmap]
rs12439525	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12441444	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443172	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593251	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs12594158	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531162	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1531163	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16972714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2229730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305667	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs28397782	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28431073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28577988	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28583379	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3743484	0.81[JPT][hapmap]
rs3743486	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743487	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs3803568	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886409	1.00[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886627	0.84[AMR][1000 genomes]
rs7163332	0.86[TSI][hapmap]
rs7165811	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs8039046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9796628	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers 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 miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
2	chr15:75094600-75101200	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:75095800-75101400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:75095800-75101600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:75096200-75105200	Weak transcription	Fetal Lung	lung
7	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:75096400-75104800	Weak transcription	Right Ventricle	heart
9	chr15:75096600-75102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:75096600-75107200	Weak transcription	Gastric	stomach
11	chr15:75096600-75107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:75096800-75101600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:75096800-75101600	Weak transcription	NHDF-Ad	bronchial
14	chr15:75096800-75101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:75096800-75101800	Weak transcription	HSMM	muscle
16	chr15:75096800-75102000	Weak transcription	NHLF	lung
17	chr15:75096800-75102200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:75096800-75102400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:75096800-75104800	Weak transcription	Ovary	ovary
20	chr15:75096800-75107200	Weak transcription	Pancreas	Pancrea
21	chr15:75096800-75107200	Weak transcription	A549	lung
22	chr15:75096800-75107400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:75096800-75107400	Weak transcription	HSMMtube	muscle
24	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
25	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
27	chr15:75096800-75109800	Weak transcription	NH-A	brain
28	chr15:75097000-75101200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:75097000-75101600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:75097000-75101600	Weak transcription	Primary B cells from cord blood	blood
31	chr15:75097000-75102800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:75097000-75107200	Weak transcription	Spleen	Spleen
33	chr15:75097000-75107600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:75097200-75101800	Weak transcription	Osteobl	bone
37	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:75097200-75109400	Weak transcription	Lung	lung
39	chr15:75097600-75101800	Weak transcription	Fetal Brain Female	brain
40	chr15:75097600-75103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:75097800-75101800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:75097800-75107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
46	chr15:75098000-75101800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:75098800-75102000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr15:75099000-75101800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr15:75099200-75101400	Enhancers	Duodenum Mucosa	Duodenum
50	chr15:75099200-75101800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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