Variant report

Variant	rs4655259
Chromosome Location	chr1:214637100-214637101
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10157143	1.00[YRI][hapmap]
rs10158378	0.91[YRI][hapmap]
rs10158490	1.00[YRI][hapmap]
rs10159086	1.00[YRI][hapmap]
rs10159464	1.00[YRI][hapmap]
rs10494980	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746445	0.83[CHB][hapmap]
rs10864100	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864101	1.00[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864102	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120329	0.85[CHB][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120330	0.85[CHB][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120331	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120332	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120333	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068677	0.85[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096551	0.82[CHB][hapmap]
rs12128034	0.84[CHB][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739305	0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739336	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12743237	0.85[CHB][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757776	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs17790515	1.00[YRI][hapmap]
rs17790562	1.00[YRI][hapmap]
rs4145623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233303	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233305	0.85[CHB][hapmap]
rs4233306	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253890	0.81[MEX][hapmap]
rs4269744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480328	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4571940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4655250	0.85[CHB][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655251	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655252	0.85[CHB][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655253	0.85[CHB][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655254	0.85[CHB][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655255	0.84[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655256	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655347	0.85[CHB][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655348	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655349	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655350	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655352	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655355	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5020616	0.85[CHB][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5020617	0.85[CHB][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540830	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540835	0.85[CHB][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540836	0.84[CHB][hapmap]
rs6540838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540841	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661786	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668440	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671350	0.80[CEU][hapmap]
rs6676807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676956	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677050	0.86[MEX][hapmap]
rs6682627	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs6682847	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684018	1.00[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691633	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518513	0.83[CHB][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540188	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540288	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4655259	SMYD2	cis	brain	seeQTL
rs4655259	PTPN14	cis	parietal	SCAN
rs4655259	PDLIM3	trans	brain	seeQTL
rs4655259	MBOAT7	trans	brain	seeQTL
rs4655259	SNCG	trans	brain	seeQTL
rs4655259	MAPRE3	trans	brain	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214613000-214649400	Weak transcription	Lung	lung
2	chr1:214620000-214637400	Weak transcription	Fetal Brain Male	brain
3	chr1:214620800-214637800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:214621000-214639800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:214625800-214644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:214627200-214640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:214628600-214637600	Weak transcription	Ovary	ovary
8	chr1:214628600-214637800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:214628600-214637800	Weak transcription	Placenta	Placenta
10	chr1:214628600-214640600	Weak transcription	Right Atrium	heart
11	chr1:214628800-214639400	Weak transcription	Stomach Mucosa	stomach
12	chr1:214629000-214637800	Weak transcription	Right Ventricle	heart
13	chr1:214629200-214644800	Weak transcription	Psoas Muscle	Psoas
14	chr1:214633600-214638000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:214634000-214638600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:214634200-214638000	Weak transcription	Pancreas	Pancrea
17	chr1:214634200-214640000	Weak transcription	Fetal Kidney	kidney
18	chr1:214634400-214637800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:214634400-214639800	Weak transcription	Fetal Lung	lung
20	chr1:214634400-214639800	Weak transcription	A549	lung
21	chr1:214634400-214640000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:214634400-214644400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:214634400-214645000	Weak transcription	HUVEC	blood vessel
24	chr1:214634400-214646200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:214634600-214637600	Strong transcription	Fetal Stomach	stomach
26	chr1:214634800-214638200	Strong transcription	Fetal Intestine Large	intestine
27	chr1:214634800-214640000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:214635000-214637800	Weak transcription	Spleen	Spleen
29	chr1:214635000-214638400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:214635000-214638600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:214635200-214637200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:214635200-214638400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:214635600-214637800	Weak transcription	Gastric	stomach
34	chr1:214635600-214638000	Genic enhancers	HMEC	breast
35	chr1:214635800-214637200	Genic enhancers	NHDF-Ad	bronchial
36	chr1:214635800-214638200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:214635800-214645000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:214636000-214637200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:214636000-214637200	Enhancers	HepG2	liver
40	chr1:214636000-214637800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:214636000-214638600	Strong transcription	NHLF	lung
42	chr1:214636200-214640600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:214636400-214637800	Genic enhancers	Osteobl	bone
44	chr1:214636400-214638200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:214636400-214638600	Enhancers	Fetal Heart	heart
46	chr1:214636600-214638000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:214636800-214637200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:214636800-214637200	Strong transcription	Aorta	Aorta
49	chr1:214636800-214637200	Enhancers	Esophagus	oesophagus
50	chr1:214636800-214637200	Enhancers	Fetal Muscle Leg	muscle

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