Variant report

Variant	rs284661
Chromosome Location	chr19:41932120-41932121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41859535..41862336-chr19:41931235..41934067,2	MCF-7	breast:
2	chr19:41855338..41857886-chr19:41930107..41932844,2	K562	blood:
3	chr19:41913241..41916784-chr19:41931234..41935699,5	MCF-7	breast:
4	chr19:41928851..41930811-chr19:41931132..41933140,2	K562	blood:
5	chr19:41902636..41905103-chr19:41930716..41934044,4	MCF-7	breast:
6	chr19:41931962..41935414-chr19:41944317..41947167,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105329	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000077348	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10409485	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10413735	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10416743	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10417311	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10417997	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420556	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10422783	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10432268	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1043413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046909	0.86[CHD][hapmap]
rs1077856	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083618	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083619	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667848	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11667908	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668924	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11670583	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670668	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670725	0.88[EUR][1000 genomes]
rs11670757	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11883104	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12709849	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12980966	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13344547	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13344563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13345590	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13346603	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1473248	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs166925	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16975238	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17318596	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17318666	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967333	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1967334	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2231940	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241706	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241707	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241708	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241709	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241711	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304242	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304243	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2317131	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2569400	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2569754	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284648	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284649	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284650	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284651	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284654	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284655	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284656	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284657	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284658	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284663	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213860	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213861	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745290	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745292	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786553	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810174	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816037	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826713	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4605279	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4674	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802116	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802117	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802118	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803462	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803463	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803467	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803468	0.86[CEU][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803469	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55986560	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58961854	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62117461	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62117462	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6508977	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247332	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255918	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258973	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8103531	0.85[EUR][1000 genomes]
rs8105833	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs878082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs878083	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs892044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9304593	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs284661	PSG2	cis	parietal	SCAN
rs284661	ZNF233	cis	cerebellum	SCAN
rs284661	B3GNT8	cis	Nerve Tibial	GTEx
rs284661	ATP5SL	cis	lymphoblastoid	seeQTL
rs284661	BCKDHA	trans	parietal	SCAN
rs284661	PVR	cis	parietal	SCAN
rs284661	LHB	cis	parietal	SCAN
rs284661	PHLDB3	cis	parietal	SCAN
rs284661	MEGF8	cis	parietal	SCAN
rs284661	NOSIP	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41913800-41932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr19:41915200-41932600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:41915400-41932800	Weak transcription	Hela-S3	cervix
4	chr19:41915600-41932800	Weak transcription	NH-A	brain
5	chr19:41916000-41932400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:41916400-41932600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr19:41916400-41932800	Strong transcription	Brain Germinal Matrix	brain
8	chr19:41916400-41932800	Strong transcription	Fetal Brain Female	brain
9	chr19:41916400-41933000	Strong transcription	Thymus	Thymus
10	chr19:41916800-41932200	Strong transcription	Primary T cells from cord blood	blood
11	chr19:41916800-41932200	Strong transcription	Ovary	ovary
12	chr19:41918200-41932200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:41918200-41932400	Weak transcription	Right Atrium	heart
14	chr19:41918200-41932800	Strong transcription	Brain Hippocampus Middle	brain
15	chr19:41918400-41932800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:41918600-41932400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:41918600-41932800	Strong transcription	Brain Angular Gyrus	brain
18	chr19:41918800-41932600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:41918800-41932800	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr19:41921200-41933000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:41921400-41932200	Weak transcription	NHDF-Ad	bronchial
22	chr19:41924400-41932400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:41924600-41933000	Strong transcription	Brain Substantia Nigra	brain
24	chr19:41924800-41932400	Strong transcription	Dnd41	blood
25	chr19:41924800-41933000	Strong transcription	A549	lung
26	chr19:41925600-41933400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:41926600-41932800	Weak transcription	Fetal Kidney	kidney
28	chr19:41926600-41932800	Genic enhancers	Spleen	Spleen
29	chr19:41926600-41933000	Weak transcription	Fetal Brain Male	brain
30	chr19:41926800-41932600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:41927000-41932200	Weak transcription	HMEC	breast
32	chr19:41927000-41932400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:41927000-41932800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:41927400-41932600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:41927400-41932600	Strong transcription	Liver	Liver
36	chr19:41928000-41932200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:41928000-41932400	Strong transcription	NHLF	lung
38	chr19:41928000-41932600	Strong transcription	Fetal Muscle Leg	muscle
39	chr19:41928200-41932200	Strong transcription	Brain Anterior Caudate	brain
40	chr19:41929000-41932800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:41929000-41932800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:41929000-41932800	Enhancers	Fetal Heart	heart
43	chr19:41929200-41932600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:41929200-41932800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:41929200-41932800	Weak transcription	HSMM	muscle
46	chr19:41929200-41933000	Weak transcription	Psoas Muscle	Psoas
47	chr19:41929200-41933000	Weak transcription	Osteobl	bone
48	chr19:41929400-41932800	Weak transcription	GM12878-XiMat	blood
49	chr19:41929600-41932200	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:41929600-41932800	Weak transcription	Fetal Lung	lung

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