Variant report

Variant	rs7181436
Chromosome Location	chr15:45900418-45900419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45457952..45460656-chr15:45900362..45903240,2	K562	blood:
2	chr15:45895546..45897491-chr15:45899127..45901340,2	K562	blood:
3	chr15:45899647..45900569-chr8:125884333..125885038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11632553	0.83[CEU][hapmap]
rs11637984	0.83[CEU][hapmap]
rs16945097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16946621	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs17627219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1966763	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083728	1.00[CEU][hapmap]
rs3649	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55755923	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55806911	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913172	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55997350	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56081351	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56179992	0.86[ASN][1000 genomes]
rs56190351	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56259807	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56304405	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375332	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56395216	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57291883	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59593563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60351453	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60378269	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60992352	0.86[ASN][1000 genomes]
rs61209164	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68044128	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685812	1.00[CEU][hapmap]
rs7164956	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165827	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169748	1.00[JPT][hapmap]
rs7170090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7175288	0.94[CEU][hapmap]
rs7178395	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7178879	0.98[ASN][1000 genomes]
rs7179265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179903	0.98[ASN][1000 genomes]
rs72711301	0.86[ASN][1000 genomes]
rs72713103	0.86[ASN][1000 genomes]
rs72713104	0.86[ASN][1000 genomes]
rs72713105	0.86[ASN][1000 genomes]
rs72713106	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713107	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713168	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713169	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713171	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713172	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713175	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713177	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72713180	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72713182	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713185	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713191	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72713197	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72713199	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72713201	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715003	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715005	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72715008	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72715010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72715014	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72715019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72715020	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72715077	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8025407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8039784	0.83[CEU][hapmap]
rs8041902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043334	1.00[CEU][hapmap]

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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7181436	SLC30A4	cis	parietal	SCAN
rs7181436	GPR176	cis	cerebellum	SCAN
rs7181436	TMEM62	cis	cerebellum	SCAN
rs7181436	RPAP1	cis	cerebellum	SCAN
rs7181436	MGA	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45881000-45908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:45881000-45908800	Weak transcription	Esophagus	oesophagus
3	chr15:45881200-45909000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:45881600-45901800	Weak transcription	Psoas Muscle	Psoas
5	chr15:45881800-45903400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:45881800-45904800	Weak transcription	NHEK	skin
7	chr15:45882000-45908600	Weak transcription	NHLF	lung
8	chr15:45884400-45901200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:45884600-45900800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:45884800-45902200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:45885000-45902400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:45887400-45902200	Weak transcription	Fetal Brain Male	brain
13	chr15:45887600-45900600	Weak transcription	HMEC	breast
14	chr15:45888800-45904800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:45889000-45901000	Weak transcription	Aorta	Aorta
16	chr15:45889000-45903600	Weak transcription	Thymus	Thymus
17	chr15:45889400-45902200	Weak transcription	K562	blood
18	chr15:45889600-45906600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:45889800-45901000	Weak transcription	Fetal Kidney	kidney
20	chr15:45889800-45904800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:45889800-45905400	Weak transcription	Fetal Intestine Small	intestine
22	chr15:45889800-45908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:45890000-45901400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:45890200-45908800	Weak transcription	A549	lung
25	chr15:45895600-45902200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:45896600-45901600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:45896600-45902000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr15:45896600-45903000	Weak transcription	Spleen	Spleen
29	chr15:45896800-45900800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:45896800-45901800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:45896800-45902000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:45896800-45902200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:45896800-45912400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:45897000-45901000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:45897000-45902000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:45897200-45901400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:45897600-45902200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:45897800-45900800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:45897800-45902200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:45898000-45900800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:45898000-45900800	Strong transcription	Adipose Nuclei	Adipose
42	chr15:45898000-45900800	Strong transcription	Brain Germinal Matrix	brain
43	chr15:45898000-45900800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:45898000-45900800	Strong transcription	Dnd41	blood
45	chr15:45898000-45901000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:45898000-45902000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:45898000-45902000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:45898000-45902000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:45898000-45903000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:45898200-45900800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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