Variant report

Variant	rs28633493
Chromosome Location	chr15:43263307-43263308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518779	1.00[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12898255	0.82[AMR][1000 genomes]
rs16957168	0.88[ASW][hapmap];0.95[CEU][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap]
rs16957422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2176870	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs2412748	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28374998	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28494835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28564939	0.85[AFR][1000 genomes]
rs28581361	0.88[AFR][1000 genomes]
rs28609797	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28613047	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28796057	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28810091	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28871732	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35838915	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3759792	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4274403	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924699	0.84[CEU][hapmap]
rs4924705	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs66947001	0.82[EUR][1000 genomes]
rs7166705	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7170376	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7176957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7178248	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181859	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182650	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8028785	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs8036674	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037022	0.83[YRI][hapmap]
rs8037613	0.84[CEU][hapmap]
rs8041432	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9920061	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920182	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920202	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1050987	chr15:43237103-43385515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv542369	chr15:43237103-43385515	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv3421859	chr15:43249285-43280570	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28633493	MAP1A	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43232000-43362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43236000-43268400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43241200-43269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:43241600-43271000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:43241600-43271800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:43241800-43270800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:43242200-43270800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:43243800-43265000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:43244000-43276400	Weak transcription	Psoas Muscle	Psoas
10	chr15:43244600-43266200	Weak transcription	Gastric	stomach
11	chr15:43248000-43320600	Weak transcription	Stomach Mucosa	stomach
12	chr15:43248200-43265000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:43249400-43265000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:43249400-43268800	Strong transcription	Fetal Muscle Leg	muscle
15	chr15:43249600-43265000	Weak transcription	A549	lung
16	chr15:43249600-43283200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:43250000-43264800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:43251400-43269800	Strong transcription	Fetal Thymus	thymus
19	chr15:43252400-43298400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:43252600-43265000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:43252800-43263400	Weak transcription	Hela-S3	cervix
22	chr15:43252800-43264000	Weak transcription	HSMMtube	muscle
23	chr15:43252800-43295800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:43253000-43265000	Weak transcription	K562	blood
25	chr15:43253600-43265400	Weak transcription	Pancreas	Pancrea
26	chr15:43254800-43266800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:43255200-43265200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:43255200-43278800	Weak transcription	Esophagus	oesophagus
29	chr15:43255400-43263600	Weak transcription	HepG2	liver
30	chr15:43256000-43265000	Weak transcription	Spleen	Spleen
31	chr15:43256200-43264400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:43257200-43265400	Weak transcription	Aorta	Aorta
33	chr15:43257400-43268800	Weak transcription	Small Intestine	intestine
34	chr15:43258400-43264200	Weak transcription	Brain Anterior Caudate	brain
35	chr15:43258400-43265000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:43258400-43265000	Weak transcription	NHLF	lung
37	chr15:43258600-43263400	Weak transcription	Ovary	ovary
38	chr15:43258600-43264200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:43258600-43264200	Weak transcription	NHDF-Ad	bronchial
40	chr15:43258600-43264400	Weak transcription	GM12878-XiMat	blood
41	chr15:43258600-43264800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:43258600-43264800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:43258600-43264800	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:43258600-43265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:43258600-43265000	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:43258600-43265000	Weak transcription	Dnd41	blood
47	chr15:43258600-43265000	Weak transcription	HUVEC	blood vessel
48	chr15:43258600-43265200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:43258600-43265400	Weak transcription	NH-A	brain
50	chr15:43258600-43266800	Weak transcription	HMEC	breast

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