Variant report

Variant	rs16962017
Chromosome Location	chr15:49339218-49339219
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr15:49336274-49339327	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr15:49337412-49339761	SK-N-SH	brain:	n/a	chr15:49338874-49338883
3	POLR2A	chr15:49337623-49339348	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr15:49338261-49339613	IMR90	lung:	n/a	n/a
5	HCFC1	chr15:49338223-49339227	K562	blood:	n/a	n/a
6	JUN	chr15:49337967-49340325	K562	blood:	n/a	n/a
7	BHLHE40	chr15:49337629-49339322	GM12878	blood:	n/a	chr15:49338296-49338312
8	TCF7L2	chr15:49338436-49339282	PANC-1	pancreas:	n/a	chr15:49338976-49338985
9	REST	chr15:49337730-49339309	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr15:49337917-49339291	SK-N-SH	brain:	n/a	chr15:49338876-49338889
11	SMC3	chr15:49337910-49339235	SK-N-SH	brain:	n/a	n/a
12	MAZ	chr15:49337232-49339570	IMR90	lung:	n/a	n/a
13	GTF2F1	chr15:49338515-49339258	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:49337821-49339335	GM12891	blood:	n/a	n/a
15	POLR2A	chr15:49337905-49339290	GM12878	blood:	n/a	n/a
16	SMARCC1	chr15:49338042-49339393	Hela-S3	cervix:	n/a	n/a
17	CHD1	chr15:49336525-49339502	IMR90	lung:	n/a	n/a
18	CTCF	chr15:49338429-49339292	A549	lung:	n/a	chr15:49338876-49338889
19	POLR2A	chr15:49338239-49339228	U87	brain:	n/a	n/a
20	ARID3A	chr15:49338428-49339343	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:49338335..49339313-chr16:3070214..3070860,2	Hela-S3	cervix:
2	chr15:49169135..49171903-chr15:49338835..49340403,2	K562	blood:
3	chr15:49337641..49340367-chr15:49461061..49463741,3	MCF-7	breast:

Variant related genes	Relation type
SECISBP2L	TF binding region
RN7SL577P	TF binding region
ENSG00000235883	Chromatin interaction
ENSG00000006327	Chromatin interaction
ENSG00000255302	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000185634	Chromatin interaction
ENSG00000264210	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1054307	0.88[JPT][hapmap]
rs11638215	0.93[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11639379	0.80[AMR][1000 genomes]
rs11855740	0.88[JPT][hapmap]
rs11858917	0.82[AMR][1000 genomes]
rs12904344	0.88[CEU][hapmap]
rs12909616	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12916287	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4284578	0.88[JPT][hapmap]
rs4390538	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs4423366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536401	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4775795	0.88[JPT][hapmap]
rs6493346	0.93[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[ASN][1000 genomes]
rs7165264	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7167402	0.88[JPT][hapmap]
rs8029751	0.87[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs8029914	0.82[JPT][hapmap]
rs8033060	0.92[CEU][hapmap];0.88[MEX][hapmap]
rs877007	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs935003	0.80[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16962017	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs16962017	DUOXA1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49336200-49339400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:49336200-49339800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:49336400-49339400	Active TSS	Brain Angular Gyrus	brain
4	chr15:49336800-49339400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:49336800-49339400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr15:49337000-49339400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:49337200-49339400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:49337200-49339400	Active TSS	Colon Smooth Muscle	Colon
9	chr15:49337400-49339400	Active TSS	Colonic Mucosa	Colon
10	chr15:49337600-49339400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr15:49337600-49339400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:49337600-49339400	Active TSS	Rectal Smooth Muscle	rectum
13	chr15:49337600-49339800	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr15:49337800-49339400	Active TSS	Duodenum Mucosa	Duodenum
15	chr15:49337800-49339400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr15:49338000-49339400	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr15:49338200-49339400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr15:49338600-49339400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:49338800-49339400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:49338800-49339400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr15:49338800-49339400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr15:49338800-49339400	Flanking Active TSS	K562	blood
23	chr15:49338800-49339400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr15:49338800-49339800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:49339000-49339400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr15:49339000-49339400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr15:49339000-49339400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:49339000-49339400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:49339000-49339400	Flanking Active TSS	A549	lung
30	chr15:49339000-49339400	Flanking Active TSS	HepG2	liver
31	chr15:49339000-49339400	Flanking Active TSS	NHEK	skin
32	chr15:49339200-49339400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:49339200-49339400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:49339200-49339400	Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr15:49339200-49339400	Enhancers	Primary B cells from cord blood	blood
36	chr15:49339200-49339400	Enhancers	Primary B cells from peripheral blood	blood
37	chr15:49339200-49339400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr15:49339200-49339400	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:49339200-49339400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:49339200-49339400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:49339200-49339400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:49339200-49339400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:49339200-49339400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr15:49339200-49339400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:49339200-49339400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:49339200-49339400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:49339200-49339400	Enhancers	Liver	Liver
48	chr15:49339200-49339400	Enhancers	Brain Cingulate Gyrus	brain
49	chr15:49339200-49339400	Enhancers	Brain Germinal Matrix	brain
50	chr15:49339200-49339400	Flanking Active TSS	Brain Hippocampus Middle	brain

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