Variant report

Variant	rs520949
Chromosome Location	chr15:49531192-49531193
allele	C/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	RAD21	chr15:49529885-49532387	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr15:49530268-49531738	SK-N-SH	brain:	n/a	n/a
3	EP300	chr15:49529875-49532539	SK-N-SH	brain:	n/a	chr15:49531958-49531972 chr15:49530330-49530344
4	NFIC	chr15:49530367-49531250	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49461247..49464422-chr15:49530030..49534036,3	K562	blood:

Variant related genes	Relation type
GALK2	TF binding region
ENSG00000264210	Chromatin interaction
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10851475	0.81[GIH][hapmap]
rs11070681	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs11070686	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631040	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap]
rs11636671	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636795	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11852524	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap]
rs11858114	0.92[GIH][hapmap]
rs12101599	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap]
rs12440534	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898709	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12900001	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs12913745	0.82[CHB][hapmap]
rs12917024	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1904317	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086256	0.95[GIH][hapmap]
rs2127242	0.95[GIH][hapmap]
rs2219812	0.95[GIH][hapmap]
rs2243899	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246995	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2413936	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413939	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413942	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2580924	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940747	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3098614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3098620	0.92[GIH][hapmap]
rs3105861	0.84[YRI][hapmap]
rs3105865	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105867	0.95[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4316697	0.82[ASW][hapmap]
rs4775803	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485182	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs532209	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568994	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs586758	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641077	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493363	0.95[GIH][hapmap]
rs6493364	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493369	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs8032650	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041781	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041823	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920772	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv569340	chr15:49529302-49547735	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv569341	chr15:49529302-49547790	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv569342	chr15:49529302-49549943	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv569343	chr15:49531192-49547790	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs520949	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs520949	DTWD1	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
2	chr15:49487200-49531200	Weak transcription	HMEC	breast
3	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
4	chr15:49508800-49535800	Weak transcription	A549	lung
5	chr15:49510000-49541800	Weak transcription	NHEK	skin
6	chr15:49510200-49537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:49510800-49534400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:49511800-49531400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:49511800-49532200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:49516000-49531400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:49518000-49535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:49518000-49541000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
14	chr15:49518600-49532000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
16	chr15:49518800-49539200	Weak transcription	Ovary	ovary
17	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
18	chr15:49520600-49531200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:49520800-49531400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:49522000-49534600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:49522000-49537800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:49522000-49538200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:49522000-49540400	Weak transcription	Stomach Mucosa	stomach
24	chr15:49522200-49531400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:49522200-49535000	Weak transcription	Left Ventricle	heart
26	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
27	chr15:49522600-49534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:49522600-49535200	Weak transcription	Gastric	stomach
29	chr15:49522800-49531400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:49523800-49534800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:49523800-49540200	Weak transcription	Spleen	Spleen
32	chr15:49524600-49531400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:49524600-49531400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:49524600-49531400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:49524600-49535200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:49524600-49535200	Weak transcription	Placenta	Placenta
37	chr15:49524600-49535200	Weak transcription	Thymus	Thymus
38	chr15:49524600-49539200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:49524600-49544800	Weak transcription	Lung	lung
40	chr15:49524800-49531400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:49525000-49531400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:49525000-49534600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:49525200-49531400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:49525200-49531400	Weak transcription	HepG2	liver
45	chr15:49525200-49535000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:49525200-49535000	Weak transcription	Fetal Intestine Large	intestine
47	chr15:49525400-49535200	Weak transcription	Fetal Intestine Small	intestine
48	chr15:49526200-49531200	Weak transcription	Primary B cells from cord blood	blood
49	chr15:49526200-49531200	Weak transcription	Primary T cells from cord blood	blood
50	chr15:49526200-49534600	Weak transcription	K562	blood

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