Variant report

Variant	rs13404037
Chromosome Location	chr2:180028655-180028656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180027947..180030148-chr2:180031681..180034023,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10084229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10084475	0.88[ASN][1000 genomes]
rs10170430	0.85[ASN][1000 genomes]
rs10196577	0.85[ASN][1000 genomes]
rs10197425	0.89[CHD][hapmap];0.86[GIH][hapmap];0.82[ASN][1000 genomes]
rs10205477	0.97[ASN][1000 genomes]
rs10208593	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10439300	0.89[JPT][hapmap]
rs10803924	0.88[JPT][hapmap]
rs10930855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10930856	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12621023	0.89[JPT][hapmap]
rs12693175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693180	0.81[EUR][1000 genomes]
rs12997079	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13022867	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13403231	1.00[ASN][1000 genomes]
rs13420572	0.88[ASN][1000 genomes]
rs13420582	0.85[ASN][1000 genomes]
rs13427714	0.82[EUR][1000 genomes]
rs17363260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454311	0.89[JPT][hapmap]
rs1900338	0.88[ASN][1000 genomes]
rs2289993	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2289994	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28763731	1.00[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs340332	0.89[JPT][hapmap]
rs340334	0.89[JPT][hapmap]
rs34728717	0.88[ASN][1000 genomes]
rs56029204	0.87[ASN][1000 genomes]
rs56109193	0.88[ASN][1000 genomes]
rs56181927	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67028844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288025	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13404037	OSBPL6	cis	parietal	SCAN
rs13404037	HOXD9	cis	parietal	SCAN
rs13404037	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs13404037	SESTD1	cis	parietal	SCAN
rs13404037	SESTD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
4	chr2:179980000-180038800	Weak transcription	HMEC	breast
5	chr2:179980000-180056800	Weak transcription	HSMM	muscle
6	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
8	chr2:179996200-180047600	Weak transcription	NH-A	brain
9	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
10	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
13	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
14	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
17	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
18	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
19	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
22	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
24	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
26	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
27	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:180007400-180035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
32	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
33	chr2:180007600-180030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:180007600-180031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:180007600-180031200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:180008400-180030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:180008600-180029400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:180008600-180037600	Weak transcription	Fetal Thymus	thymus
40	chr2:180008600-180038400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
42	chr2:180011200-180029000	Weak transcription	Dnd41	blood
43	chr2:180011800-180039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
45	chr2:180015000-180041600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:180015000-180043200	Weak transcription	Gastric	stomach
47	chr2:180015000-180054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:180015000-180060600	Weak transcription	Lung	lung
50	chr2:180015200-180039600	Weak transcription	Fetal Lung	lung

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