Variant report

Variant	rs17454311
Chromosome Location	chr2:180024167-180024168
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10084475	0.94[AFR][1000 genomes]
rs10164707	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs10164814	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10173710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10181464	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs10188759	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10196366	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10208593	0.86[ASW][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10209887	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs1159257	1.00[CHB][hapmap]
rs12615736	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617002	0.81[CHD][hapmap]
rs12621023	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs12621115	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs12622075	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap]
rs12693175	0.89[JPT][hapmap]
rs12693178	0.83[LWK][hapmap];0.92[YRI][hapmap]
rs12693179	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs12987285	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs13029576	0.88[JPT][hapmap]
rs13382185	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs13392996	0.83[EUR][1000 genomes]
rs13396334	0.89[JPT][hapmap]
rs13403102	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13404037	0.89[JPT][hapmap]
rs13417919	0.83[EUR][1000 genomes]
rs17363260	0.89[JPT][hapmap]
rs1900338	0.86[AFR][1000 genomes]
rs1968618	0.89[YRI][hapmap]
rs2289993	1.00[ASW][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2289994	1.00[ASW][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2655153	0.83[EUR][1000 genomes]
rs28763731	0.91[AFR][1000 genomes]
rs340354	0.84[EUR][1000 genomes]
rs340355	0.84[EUR][1000 genomes]
rs34728717	0.86[AFR][1000 genomes]
rs4894081	0.82[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs56109193	0.93[AFR][1000 genomes]
rs67312569	0.85[AFR][1000 genomes]
rs6743412	0.84[CEU][hapmap]
rs6759983	0.84[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap]
rs7569887	0.82[CHD][hapmap]
rs7601366	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs7608745	0.84[CEU][hapmap]
rs9288025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9288026	0.94[CEU][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17454311	SESTD1	cis	multi-tissue	Pritchard
rs17454311	SESTD1	cis	cerebellum	SCAN
rs17454311	HOXD9	cis	parietal	SCAN
rs17454311	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs17454311	OSBPL6	cis	parietal	SCAN
rs17454311	SESTD1	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
7	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
9	chr2:179996200-180047600	Weak transcription	NH-A	brain
10	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
11	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
13	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
14	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
15	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
18	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
19	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
20	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
21	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
23	chr2:180006200-180031400	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:180006200-180031400	Weak transcription	Fetal Brain Female	brain
25	chr2:180006400-180030200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
27	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
28	chr2:180006800-180031600	Weak transcription	Brain Anterior Caudate	brain
29	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:180007200-180028600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:180007400-180035200	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:180007400-180035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
34	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
35	chr2:180007600-180030400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:180007600-180031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:180007600-180031200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:180008400-180030600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:180008600-180028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:180008600-180029400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:180008600-180037600	Weak transcription	Fetal Thymus	thymus
43	chr2:180008600-180038400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
45	chr2:180009000-180026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:180011200-180029000	Weak transcription	Dnd41	blood
47	chr2:180011800-180039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
49	chr2:180014600-180027800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:180015000-180028600	Weak transcription	Muscle Satellite Cultured Cells	--

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