Variant report

Variant	rs8028258
Chromosome Location	chr15:52022355-52022356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52015670..52018450-chr15:52021031..52024231,3	K562	blood:
2	chr15:51912795..51914902-chr15:52021958..52024650,2	K562	blood:
3	chr15:52018882..52021181-chr15:52022278..52024418,2	K562	blood:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1035737	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs10444798	0.88[AMR][1000 genomes]
rs10444823	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10775145	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070864	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070865	0.89[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs11070868	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs1133882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11630084	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11630943	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs11632106	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11636345	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637876	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs11638161	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11638766	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11638820	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12903707	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905283	0.83[ASW][hapmap];0.84[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes]
rs12908327	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs12917133	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1350174	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1466276	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1545602	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17526463	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs17526760	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs17611193	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs1811326	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1840708	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs1867984	1.00[CEU][hapmap]
rs1902430	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs1972689	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2006772	0.83[EUR][1000 genomes]
rs2007355	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs2014638	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2034856	0.83[ASW][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap]
rs2034857	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2034858	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2077743	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168475	0.88[ASN][1000 genomes]
rs2252831	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2264339	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2303443	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs2414116	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2414117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414119	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2433217	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs2433221	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs2436661	0.83[EUR][1000 genomes]
rs2441780	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2448946	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs2554305	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554306	0.85[EUR][1000 genomes]
rs2554307	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554327	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2554332	1.00[CEU][hapmap]
rs2554336	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs2554349	0.83[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2554354	0.84[CEU][hapmap]
rs2554355	0.82[CEU][hapmap]
rs2570224	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs2570228	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs2570231	0.82[EUR][1000 genomes]
rs2570233	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2570235	0.84[EUR][1000 genomes]
rs2570236	0.82[EUR][1000 genomes]
rs2570237	0.82[EUR][1000 genomes]
rs2570239	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2570241	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs2570243	0.85[CEU][hapmap]
rs2570251	0.83[EUR][1000 genomes]
rs2570252	1.00[CEU][hapmap]
rs2570253	1.00[CEU][hapmap]
rs2570258	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs2593173	0.86[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2623245	0.82[CEU][hapmap]
rs2623247	0.85[CEU][hapmap]
rs2623251	0.85[CEU][hapmap]
rs2623254	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2623259	1.00[CEU][hapmap]
rs2623263	0.85[CEU][hapmap]
rs2623270	0.82[CEU][hapmap]
rs2623271	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2912189	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs2916172	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2916176	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2929425	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2929426	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs2959285	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2959298	0.83[TSI][hapmap]
rs3088312	0.82[AMR][1000 genomes]
rs3751596	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794530	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3794534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794535	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794536	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4238383	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4502160	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4534783	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4622456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774602	0.89[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775978	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775982	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775983	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs526556	0.87[ASN][1000 genomes]
rs55843525	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55887408	0.85[EUR][1000 genomes]
rs6493515	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493518	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493519	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493520	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs6493522	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493523	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493525	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs6493526	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs689884	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7163176	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165283	1.00[CEU][hapmap]
rs7165585	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166110	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7166962	0.85[AMR][1000 genomes]
rs7168659	0.85[AMR][1000 genomes]
rs7171459	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173375	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7174497	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7174808	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7174941	0.85[EUR][1000 genomes]
rs7181553	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7182917	0.82[EUR][1000 genomes]
rs8024081	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024088	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024589	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026521	0.91[AMR][1000 genomes]
rs8027721	0.85[AMR][1000 genomes]
rs8028890	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8028922	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs8035173	0.86[GIH][hapmap]
rs8041268	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8028258	TMOD2	cis	cerebellum	SCAN
rs8028258	SCG3	cis	Cerebellum	GTEx
rs8028258	SCG3	cis	Temporal Cortex	GTEx
rs8028258	GNB5	cis	lymphoblastoid	seeQTL
rs8028258	SCG3	cis	cerebellum	SCAN
rs8028258	TMOD2	cis	parietal	SCAN
rs8028258	SCG3	cis	Brain Pons	GTEx
rs8028258	LYSMD2	cis	Muscle Skeletal	GTEx
rs8028258	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52000800-52024000	Weak transcription	Gastric	stomach
2	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
3	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:52011400-52023400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:52011600-52023400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:52012400-52024200	Weak transcription	Fetal Lung	lung
8	chr15:52013400-52023600	Weak transcription	Colonic Mucosa	Colon
9	chr15:52013600-52028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:52013600-52028400	Weak transcription	Fetal Brain Female	brain
11	chr15:52013600-52028800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:52014000-52023000	Weak transcription	Stomach Mucosa	stomach
13	chr15:52014600-52022600	Weak transcription	Fetal Thymus	thymus
14	chr15:52014800-52023000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:52016800-52023000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr15:52017200-52022400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:52017200-52022400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:52017200-52022800	Weak transcription	Liver	Liver
19	chr15:52017200-52023400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:52017400-52022400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:52017400-52022400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:52017400-52023600	Weak transcription	Placenta	Placenta
23	chr15:52017600-52023400	Weak transcription	Fetal Intestine Large	intestine
24	chr15:52018400-52023000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr15:52019000-52023600	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:52019000-52023800	Weak transcription	Brain Angular Gyrus	brain
27	chr15:52019000-52028200	Weak transcription	Brain Substantia Nigra	brain
28	chr15:52019200-52023400	Weak transcription	Adipose Nuclei	Adipose
29	chr15:52019200-52023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:52019400-52023000	Weak transcription	Fetal Intestine Small	intestine
31	chr15:52019400-52023600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:52019400-52023800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:52019600-52023200	Weak transcription	Fetal Stomach	stomach
34	chr15:52019600-52024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:52019800-52023000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr15:52019800-52023600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:52019800-52023600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:52019800-52023800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:52019800-52023800	Weak transcription	Aorta	Aorta
40	chr15:52020000-52022400	Weak transcription	Lung	lung
41	chr15:52020000-52022400	Weak transcription	Thymus	Thymus
42	chr15:52020000-52022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:52020000-52023200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:52020000-52023200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:52020000-52023200	Weak transcription	HSMMtube	muscle
46	chr15:52020000-52023200	Weak transcription	NHEK	skin
47	chr15:52020000-52023400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:52020000-52023400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:52020000-52023600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:52020000-52023600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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