Variant report

Variant	rs17581284
Chromosome Location	chr2:172659376-172659377
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	chr2:172653773..172656691-chr2:172656792..172659736,2	K562	blood:
2	chr2:172656554..172659415-chr2:172948185..172950297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1028127	0.87[EUR][1000 genomes]
rs10930491	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11690807	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052995	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12997093	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12998411	0.87[EUR][1000 genomes]
rs1607254	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17614941	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271758	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292816	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34242651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34531723	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35854151	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4510184	0.85[AMR][1000 genomes]
rs59844139	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62184165	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6723259	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9789538	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17581284	AC068039.4	cis	Esophagus Muscularis	GTEx
rs17581284	SLC25A12	cis	cerebellum	SCAN
rs17581284	SLC25A12	cis	parietal	SCAN
rs17581284	AC068039.4	cis	Thyroid	GTEx
rs17581284	MAP1D	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:172640200-172662800	Weak transcription	Fetal Brain Male	brain
3	chr2:172640400-172668000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:172641600-172666400	Weak transcription	Fetal Kidney	kidney
5	chr2:172642200-172663600	Weak transcription	K562	blood
6	chr2:172642200-172665800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:172642400-172688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:172643600-172687800	Weak transcription	Hela-S3	cervix
9	chr2:172643800-172674600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:172644000-172667000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:172644200-172666600	Weak transcription	Placenta	Placenta
12	chr2:172644400-172666000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:172644400-172681800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:172644400-172684400	Weak transcription	Spleen	Spleen
15	chr2:172644600-172681800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:172645400-172687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:172648200-172666000	Weak transcription	Fetal Brain Female	brain
18	chr2:172648200-172684400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:172648200-172687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:172648200-172687400	Weak transcription	Colonic Mucosa	Colon
21	chr2:172648400-172671000	Weak transcription	Psoas Muscle	Psoas
22	chr2:172648400-172671200	Weak transcription	Right Ventricle	heart
23	chr2:172648400-172681800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:172648400-172687600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:172648800-172687400	Weak transcription	Esophagus	oesophagus
26	chr2:172649000-172687400	Weak transcription	Gastric	stomach
27	chr2:172649200-172682000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:172650200-172662400	Weak transcription	Ovary	ovary
29	chr2:172650400-172661000	Weak transcription	Fetal Stomach	stomach
30	chr2:172650400-172665600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:172650400-172666000	Weak transcription	GM12878-XiMat	blood
32	chr2:172650400-172666600	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:172650400-172671200	Weak transcription	Adipose Nuclei	Adipose
34	chr2:172650400-172671400	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:172650400-172680200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:172650400-172681800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:172650400-172687400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:172650400-172687600	Weak transcription	Lung	lung
39	chr2:172650600-172663200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:172650600-172669800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:172650800-172659400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:172651000-172661200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:172651000-172664200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:172651800-172662200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:172651800-172664200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:172651800-172682000	Weak transcription	Fetal Thymus	thymus
47	chr2:172652000-172666800	Weak transcription	Brain Germinal Matrix	brain
48	chr2:172652400-172663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:172652400-172664400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:172653000-172687400	Weak transcription	Fetal Heart	heart

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