Variant report

Variant	rs3132671
Chromosome Location	chr6:30178287-30178288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30176086..30179759-chr6:30179877..30183202,4	K562	blood:
2	chr6:30175583..30179292-chr6:30184478..30187344,3	K562	blood:
3	chr6:30177177..30179717-chr6:30228563..30230650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1362089	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1573295	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2021365	0.83[EUR][1000 genomes]
rs2021366	0.82[ASN][1000 genomes]
rs2074472	0.91[ASN][1000 genomes]
rs2074473	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097772	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2106070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106071	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107196	0.86[ASN][1000 genomes]
rs2158283	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2253163	0.82[ASN][1000 genomes]
rs2253164	0.82[ASN][1000 genomes]
rs2284164	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285801	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285802	0.83[EUR][1000 genomes]
rs2394737	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2394778	0.83[EUR][1000 genomes]
rs2428503	0.81[AFR][1000 genomes]
rs2428505	0.84[EUR][1000 genomes]
rs2508029	0.87[ASN][1000 genomes]
rs2516723	0.84[EUR][1000 genomes]
rs2517611	0.81[AFR][1000 genomes]
rs2517614	0.83[AFR][1000 genomes]
rs2523713	0.81[AFR][1000 genomes]
rs2523722	0.83[AFR][1000 genomes]
rs28398051	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28441239	0.90[ASN][1000 genomes]
rs2844767	0.84[EUR][1000 genomes]
rs2844768	0.84[EUR][1000 genomes]
rs2844778	0.86[ASN][1000 genomes]
rs2844782	0.87[ASN][1000 genomes]
rs2844786	0.87[ASN][1000 genomes]
rs3094130	0.83[EUR][1000 genomes]
rs3094131	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094139	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3094140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094615	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094635	0.83[EUR][1000 genomes]
rs3094636	0.83[EUR][1000 genomes]
rs3094639	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129694	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130381	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130382	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130383	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130384	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130386	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130387	0.86[ASN][1000 genomes]
rs3130388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130389	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130393	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130394	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3132664	0.82[EUR][1000 genomes]
rs3132665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132669	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132672	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132673	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132674	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35848695	0.81[ASN][1000 genomes]
rs4959046	0.82[ASN][1000 genomes]
rs6457164	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457165	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457167	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs718254	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7382110	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7383511	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757257	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765977	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7763162	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7764012	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774730	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs885914	0.89[ASN][1000 genomes]
rs885915	0.91[ASN][1000 genomes]
rs916568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916571	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916572	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261539	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261543	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261546	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261548	0.86[ASN][1000 genomes]
rs9261592	0.83[EUR][1000 genomes]
rs971570	0.81[AFR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3132671	GRM4	cis	cerebellum	SCAN
rs3132671	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
3	chr6:30168800-30179800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:30169000-30179800	Weak transcription	Aorta	Aorta
5	chr6:30170200-30179200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:30170600-30179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:30172400-30179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:30172600-30178400	Enhancers	Esophagus	oesophagus
9	chr6:30172600-30179800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:30173000-30179200	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr6:30173200-30178400	Enhancers	Pancreas	Pancrea
12	chr6:30173400-30179600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:30173400-30179800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:30173400-30179800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:30173800-30179800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:30173800-30180000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:30174600-30180400	Enhancers	Small Intestine	intestine
18	chr6:30174800-30179200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:30175000-30179200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:30175000-30179200	Enhancers	Fetal Intestine Small	intestine
21	chr6:30175000-30179800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:30175400-30179000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:30175400-30180000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:30175600-30178800	Weak transcription	Fetal Thymus	thymus
25	chr6:30175800-30179000	Weak transcription	HSMMtube	muscle
26	chr6:30175800-30179400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:30175800-30179800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:30175800-30179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:30175800-30180400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:30175800-30180400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:30175800-30180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:30176000-30178600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:30176000-30179200	Weak transcription	NH-A	brain
34	chr6:30176000-30179400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:30176200-30178400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:30176200-30178600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:30176200-30178600	Weak transcription	Adipose Nuclei	Adipose
38	chr6:30176200-30178600	Weak transcription	Brain Substantia Nigra	brain
39	chr6:30176200-30178600	Weak transcription	Osteobl	bone
40	chr6:30176200-30178800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:30176200-30178800	Weak transcription	Left Ventricle	heart
42	chr6:30176200-30179200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:30176200-30179200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:30176200-30179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr6:30176200-30179800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:30176200-30179800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:30176200-30179800	Weak transcription	Right Ventricle	heart
48	chr6:30176200-30180600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:30176200-30180600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:30176400-30178400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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