Variant report

Variant	rs3825524
Chromosome Location	chr13:51969696-51969697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51968496..51970934-chr13:52376792..52378777,2	K562	blood:
2	chr13:51967878..51970855-chr13:52024564..52027900,3	K562	blood:
3	chr13:51966813..51968638-chr13:51968842..51971836,2	K562	blood:

Variant related genes	Relation type
ENSG00000102796	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2274061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274929	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941696	0.85[EUR][1000 genomes]
rs4942989	0.85[EUR][1000 genomes]
rs4942991	0.85[EUR][1000 genomes]
rs6561634	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321642	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7333661	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335141	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7989850	0.82[CEU][hapmap]
rs7996243	1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7998084	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap]
rs8001311	0.81[ASN][1000 genomes]
rs9316537	0.93[ASW][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs9316539	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316545	0.82[CEU][hapmap]
rs9526752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526754	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526757	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9526764	0.81[CEU][hapmap]
rs9526765	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535645	1.00[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535653	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535669	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535670	0.82[CEU][hapmap]
rs9535672	0.81[ASN][1000 genomes]
rs9535673	0.81[ASN][1000 genomes]
rs9535674	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535677	0.81[ASN][1000 genomes]
rs9535692	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535696	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs9535697	0.81[CEU][hapmap]
rs9563051	0.86[AFR][1000 genomes]
rs9568600	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9568603	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs9568612	0.82[CEU][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3825524	INTS6	cis	lymphoblastoid	seeQTL
rs3825524	WDFY2	cis	parietal	SCAN
rs3825524	CKAP2	cis	parietal	SCAN
rs3825524	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51935600-51971400	Weak transcription	Gastric	stomach
2	chr13:51939200-51970600	Weak transcription	Brain Angular Gyrus	brain
3	chr13:51945200-51970600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:51945200-51971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:51945400-51970600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:51946200-51988000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:51946400-51971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:51947000-51970800	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:51948000-51970800	Weak transcription	A549	lung
11	chr13:51948000-51971400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:51948600-51971600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:51948600-51971600	Weak transcription	Small Intestine	intestine
14	chr13:51949000-51971400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:51949400-51971400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:51949400-51971400	Weak transcription	Esophagus	oesophagus
17	chr13:51949400-51971400	Weak transcription	Pancreas	Pancrea
18	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:51950000-51970600	Weak transcription	Brain Substantia Nigra	brain
20	chr13:51950000-51971400	Weak transcription	Fetal Stomach	stomach
21	chr13:51950000-51971400	Weak transcription	Left Ventricle	heart
22	chr13:51950000-51971800	Weak transcription	Lung	lung
23	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr13:51950200-51999800	Weak transcription	Brain Germinal Matrix	brain
25	chr13:51951800-51970600	Weak transcription	Hela-S3	cervix
26	chr13:51952400-51970600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:51952400-51971400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr13:51952600-51970800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr13:51952600-51970800	Weak transcription	HSMMtube	muscle
30	chr13:51952600-51971400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:51953200-51970600	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:51954000-51970600	Weak transcription	K562	blood
33	chr13:51955200-51973600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:51957200-51971400	Weak transcription	Fetal Intestine Small	intestine
35	chr13:51957400-51978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr13:51957800-51971600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr13:51957800-51978400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:51957800-51986600	Weak transcription	Fetal Thymus	thymus
39	chr13:51958000-51970600	Weak transcription	Adipose Nuclei	Adipose
40	chr13:51958000-51970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr13:51958000-51970800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:51958000-51971400	Weak transcription	Fetal Lung	lung
43	chr13:51958000-51971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:51958000-51971600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr13:51958000-51996800	Weak transcription	Thymus	Thymus
46	chr13:51958200-51971400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:51958200-51990000	Weak transcription	HMEC	breast
48	chr13:51958400-51987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr13:51959200-51969800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:51959200-51981200	Weak transcription	Primary B cells from peripheral blood	blood

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