Variant report

Variant	rs16957997
Chromosome Location	chr15:73845808-73845809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73844384..73847229-chr15:73925427..73927341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10152645	0.89[JPT][hapmap]
rs10162605	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10163172	0.86[EUR][1000 genomes]
rs1044581	0.88[JPT][hapmap]
rs11072433	0.88[JPT][hapmap]
rs11574484	0.88[JPT][hapmap]
rs11574485	0.88[JPT][hapmap]
rs11638472	0.82[EUR][1000 genomes]
rs11854138	0.82[CEU][hapmap]
rs11854774	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856313	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324832	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12908815	0.86[EUR][1000 genomes]
rs13380155	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13380245	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1481087	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16957919	0.80[EUR][1000 genomes]
rs16958019	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958025	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16958041	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16958050	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291012	0.88[JPT][hapmap]
rs2291014	0.88[JPT][hapmap]
rs2306462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28834466	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3889590	0.82[EUR][1000 genomes]
rs55636021	0.86[EUR][1000 genomes]
rs55695286	0.86[EUR][1000 genomes]
rs56190024	0.86[EUR][1000 genomes]
rs56227598	0.82[EUR][1000 genomes]
rs57995256	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60419012	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495066	0.82[EUR][1000 genomes]
rs7163212	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163693	0.87[CEU][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7164953	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165447	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7166673	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169976	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7172448	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7173068	0.82[EUR][1000 genomes]
rs7176174	0.89[JPT][hapmap]
rs7176452	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176484	0.89[JPT][hapmap]
rs7176701	0.88[JPT][hapmap]
rs7177731	0.85[CEU][hapmap]
rs7177814	0.88[JPT][hapmap]
rs7178133	0.88[JPT][hapmap]
rs7178806	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182876	0.89[JPT][hapmap]
rs729155	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027255	0.82[EUR][1000 genomes]
rs8028749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032265	0.82[CEU][hapmap]
rs8033242	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8036438	0.87[CEU][hapmap]
rs8039862	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8040552	0.86[ASN][1000 genomes]
rs899271	0.89[JPT][hapmap]

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	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv904344	chr15:73800519-73864831	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16957997	NMRAL1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73808200-73847400	Weak transcription	Left Ventricle	heart
2	chr15:73820800-73847600	Weak transcription	Aorta	Aorta
3	chr15:73821200-73846000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:73826800-73847600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:73827800-73847600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:73832600-73847600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:73832800-73846200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:73833000-73847600	Weak transcription	Liver	Liver
9	chr15:73833000-73848000	Weak transcription	HMEC	breast
10	chr15:73833200-73847400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:73834600-73847000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:73834600-73847400	Weak transcription	Fetal Intestine Large	intestine
13	chr15:73835000-73848400	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:73835400-73848800	Weak transcription	Primary B cells from cord blood	blood
15	chr15:73836200-73847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:73836200-73850600	Weak transcription	HUVEC	blood vessel
17	chr15:73836400-73847000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:73836800-73847400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:73836800-73847600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:73837000-73860000	Weak transcription	Gastric	stomach
21	chr15:73837200-73848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:73838200-73848600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:73838200-73850400	Weak transcription	Right Ventricle	heart
24	chr15:73838200-73851000	Weak transcription	Colonic Mucosa	Colon
25	chr15:73838800-73847200	Weak transcription	Primary T cells from cord blood	blood
26	chr15:73840800-73846400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:73842000-73847600	Weak transcription	Esophagus	oesophagus
28	chr15:73842200-73846800	Weak transcription	Fetal Stomach	stomach
29	chr15:73842400-73847400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:73842600-73847400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:73842800-73847400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:73842800-73847600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:73842800-73847600	Weak transcription	NHLF	lung
34	chr15:73843000-73846000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:73843000-73848400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:73843000-73848400	Weak transcription	Fetal Heart	heart
37	chr15:73843200-73846800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:73843400-73846600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:73843400-73847400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:73843400-73847400	Weak transcription	Spleen	Spleen
41	chr15:73843400-73849200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:73843600-73846000	Weak transcription	NHDF-Ad	bronchial
43	chr15:73843600-73847600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:73843600-73847800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:73843600-73848600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:73843800-73846000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:73843800-73847400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:73843800-73851200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:73844000-73856200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:73844200-73863800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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