Variant report

Variant	rs249414
Chromosome Location	chr5:40733694-40733695
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	chr5:40718963..40720614-chr5:40731326..40734090,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10056345	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10060234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10064175	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1057631	0.84[CEU][hapmap]
rs1070446	0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs10737963	0.83[CEU][hapmap]
rs1097546	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13354346	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13355305	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154268	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs154275	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs154280	0.87[ASN][1000 genomes]
rs154284	0.87[ASN][1000 genomes]
rs1644962	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs171605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171606	0.80[ASN][1000 genomes]
rs192219	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs193864	0.85[ASN][1000 genomes]
rs193866	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2161521	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249413	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249416	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249420	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249423	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs249429	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs257009	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs28569300	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29740	0.87[ASN][1000 genomes]
rs29742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29761	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs369940	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4133101	0.88[CEU][hapmap]
rs4277957	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4285273	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4315964	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4315965	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432071	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4345353	0.84[CEU][hapmap]
rs434778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4383756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4434423	0.84[CEU][hapmap]
rs447810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs453037	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4546432	0.87[CEU][hapmap]
rs4573034	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs457776	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4607392	0.88[CEU][hapmap]
rs461404	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs466108	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs466962	0.85[ASN][1000 genomes]
rs4957344	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59069340	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59920139	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6451535	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6451537	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6871999	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6896993	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7708680	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7711806	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]
rs7726237	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7737044	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs837101	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs249414	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs249414	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs249414	RPL37	cis	cerebellum	SCAN
rs249414		cis	Lymphoblastoid	GTEx
rs249414	Hs.506072	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:40709600-40745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:40712800-40741200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:40713200-40740600	Weak transcription	Right Ventricle	heart
7	chr5:40713600-40734800	Weak transcription	Hela-S3	cervix
8	chr5:40714600-40739400	Weak transcription	GM12878-XiMat	blood
9	chr5:40715400-40739400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:40715600-40734800	Weak transcription	NHEK	skin
11	chr5:40716400-40733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:40717800-40734400	Weak transcription	NH-A	brain
13	chr5:40721200-40733800	Weak transcription	Psoas Muscle	Psoas
14	chr5:40721200-40739600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:40721400-40735000	Weak transcription	Small Intestine	intestine
16	chr5:40721400-40739600	Weak transcription	Placenta	Placenta
17	chr5:40721400-40741400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:40721600-40733800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:40721600-40736000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:40721800-40733800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:40721800-40735800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:40721800-40738800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:40721800-40739000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:40721800-40740600	Weak transcription	Fetal Brain Male	brain
25	chr5:40722200-40739400	Weak transcription	Primary B cells from cord blood	blood
26	chr5:40722800-40735000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:40722800-40735000	Weak transcription	Esophagus	oesophagus
28	chr5:40722800-40735000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:40722800-40739200	Weak transcription	Fetal Brain Female	brain
30	chr5:40722800-40741400	Weak transcription	Aorta	Aorta
31	chr5:40722800-40755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:40723000-40741600	Weak transcription	Lung	lung
33	chr5:40723800-40735000	Weak transcription	K562	blood
34	chr5:40724200-40740600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:40724400-40737000	Weak transcription	Brain Germinal Matrix	brain
36	chr5:40724400-40738800	Weak transcription	A549	lung
37	chr5:40724600-40733800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:40724600-40734200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:40724600-40740800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:40724800-40733800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:40724800-40740600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:40726200-40734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:40728000-40735000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:40728000-40735000	Weak transcription	Osteobl	bone
45	chr5:40728000-40735600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:40728200-40733800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:40728200-40733800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:40728200-40734200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:40728200-40739000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:40728200-40745600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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