Variant report

Variant	rs2243899
Chromosome Location	chr15:49441325-49441326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49440196..49442233-chr15:49445854..49447948,2	MCF-7	breast:
2	chr15:49439437..49443597-chr15:49460944..49463407,4	MCF-7	breast:
3	chr15:49438116..49443617-chr15:49443933..49448726,7	K562	blood:
4	chr15:49411597..49414274-chr15:49439381..49441889,2	K562	blood:
5	chr15:49409539..49411389-chr15:49441274..49443184,2	MCF-7	breast:
6	chr15:49336910..49339486-chr15:49439090..49441329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264210	Chromatin interaction
ENSG00000166200	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000259467	Chromatin interaction
ENSG00000138593	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10519208	0.83[ASN][1000 genomes]
rs11070686	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11632976	0.83[ASN][1000 genomes]
rs11636671	0.84[AFR][1000 genomes]
rs11637601	0.83[ASN][1000 genomes]
rs12101442	0.82[ASN][1000 genomes]
rs12101599	0.81[ASN][1000 genomes]
rs12438357	0.81[ASN][1000 genomes]
rs12440534	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12898709	0.81[ASN][1000 genomes]
rs12917024	0.81[ASN][1000 genomes]
rs1904317	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246995	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413930	0.81[ASN][1000 genomes]
rs2413936	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413939	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2413942	0.84[AFR][1000 genomes]
rs2580924	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28505357	0.81[ASN][1000 genomes]
rs28575845	0.81[ASN][1000 genomes]
rs28790333	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2940747	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3098614	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3105865	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3105867	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4468544	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4775803	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485182	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs520949	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532209	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568994	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586758	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs641077	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493364	0.84[AFR][1000 genomes]
rs7497114	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8032650	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041781	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8041823	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920070	0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2243899	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
3	chr15:49419000-49445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:49420200-49447000	Weak transcription	Spleen	Spleen
5	chr15:49420400-49447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:49429200-49447000	Weak transcription	Esophagus	oesophagus
7	chr15:49433800-49446600	Weak transcription	Fetal Intestine Small	intestine
8	chr15:49435200-49445800	Weak transcription	Fetal Heart	heart
9	chr15:49435600-49446600	Weak transcription	Right Ventricle	heart
10	chr15:49435800-49442800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:49435800-49442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:49435800-49443000	Weak transcription	Colonic Mucosa	Colon
13	chr15:49435800-49443000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:49435800-49445400	Weak transcription	Brain Germinal Matrix	brain
15	chr15:49435800-49445600	Weak transcription	Fetal Brain Male	brain
16	chr15:49435800-49445600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:49435800-49446000	Weak transcription	Fetal Kidney	kidney
18	chr15:49435800-49446000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:49435800-49446600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:49435800-49446600	Weak transcription	HSMMtube	muscle
21	chr15:49435800-49446800	Weak transcription	Aorta	Aorta
22	chr15:49435800-49446800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:49436000-49444800	Weak transcription	Lung	lung
24	chr15:49436000-49445200	Weak transcription	Thymus	Thymus
25	chr15:49436000-49446000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:49436000-49446600	Weak transcription	Fetal Stomach	stomach
27	chr15:49436000-49446600	Weak transcription	Fetal Thymus	thymus
28	chr15:49436000-49446800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:49436000-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:49436000-49447000	Weak transcription	Gastric	stomach
31	chr15:49436000-49447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:49436200-49446600	Weak transcription	Fetal Lung	lung
33	chr15:49436200-49446600	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:49436200-49447000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:49436400-49441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:49436400-49447000	Weak transcription	Left Ventricle	heart
37	chr15:49437000-49441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:49437000-49444600	Weak transcription	Dnd41	blood
39	chr15:49437000-49446600	Weak transcription	Fetal Brain Female	brain
40	chr15:49437200-49445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:49437200-49445800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:49437200-49445800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:49437200-49445800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:49437200-49446000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:49437200-49446000	Weak transcription	Fetal Intestine Large	intestine
46	chr15:49437200-49446800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:49437400-49441400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:49437400-49441800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr15:49437400-49445000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:49437400-49446000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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