Variant report

Variant	rs765977
Chromosome Location	chr6:30157654-30157655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30157586-30157758	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30157337-30158996	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:30157545-30157686	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:30157554-30158421	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:30157292-30157679	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30156337..30158600-chr6:30180750..30182606,2	MCF-7	breast:

Variant related genes	Relation type
PAIP1P1	TF binding region
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1573295	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074472	0.95[ASN][1000 genomes]
rs2074473	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2097772	0.82[ASN][1000 genomes]
rs2106070	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106071	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2107196	0.89[ASN][1000 genomes]
rs2158283	0.91[ASN][1000 genomes]
rs2284164	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394737	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2508029	0.91[ASN][1000 genomes]
rs28441239	0.95[ASN][1000 genomes]
rs2844778	0.83[ASN][1000 genomes]
rs2844782	0.91[ASN][1000 genomes]
rs2844786	0.91[ASN][1000 genomes]
rs3094131	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094132	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094139	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3094140	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094614	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094615	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094639	0.82[ASN][1000 genomes]
rs3129694	0.80[EUR][1000 genomes]
rs3130381	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130382	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130383	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130384	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130386	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130387	0.82[ASN][1000 genomes]
rs3130388	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130389	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130391	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130393	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130394	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3132665	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3132668	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132669	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132671	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132672	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132673	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3132674	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457164	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457165	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457167	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718254	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382110	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7383511	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757257	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7763162	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7764012	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7774730	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885914	0.86[ASN][1000 genomes]
rs885915	0.88[ASN][1000 genomes]
rs916568	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs916571	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs916572	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261539	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261543	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261546	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261548	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs765977	ZKSCAN3	cis	parietal	SCAN
rs765977	GRM4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30145000-30173800	Weak transcription	Right Atrium	heart
2	chr6:30148000-30173000	Weak transcription	Fetal Heart	heart
3	chr6:30150200-30163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:30151600-30161400	Strong transcription	Primary T cells from cord blood	blood
6	chr6:30151800-30158200	Strong transcription	Brain Cingulate Gyrus	brain
7	chr6:30151800-30160400	Strong transcription	Thymus	Thymus
8	chr6:30151800-30160600	Strong transcription	Fetal Intestine Small	intestine
9	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:30152000-30159200	Strong transcription	Brain Anterior Caudate	brain
11	chr6:30152000-30160200	Strong transcription	Fetal Brain Female	brain
12	chr6:30152000-30160200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:30152000-30160400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:30152000-30160600	Strong transcription	Fetal Muscle Leg	muscle
15	chr6:30152000-30160800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:30152000-30166400	Strong transcription	Liver	Liver
17	chr6:30152000-30168000	Strong transcription	Fetal Intestine Large	intestine
18	chr6:30152000-30168200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:30152000-30168200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:30152000-30168200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:30152000-30169000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:30152200-30159200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:30152200-30159400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr6:30152200-30159600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:30152200-30159800	Strong transcription	Primary B cells from cord blood	blood
28	chr6:30152200-30159800	Strong transcription	Fetal Thymus	thymus
29	chr6:30152200-30160200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:30152200-30160200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr6:30152200-30160200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:30152200-30160400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:30152200-30160400	Strong transcription	Fetal Stomach	stomach
34	chr6:30152200-30160600	Strong transcription	Brain Hippocampus Middle	brain
35	chr6:30152200-30167800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:30152200-30167800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr6:30152200-30168000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr6:30152200-30168200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:30152200-30168200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr6:30152200-30168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:30152200-30169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:30152400-30159000	Strong transcription	HSMMtube	muscle
43	chr6:30152400-30160200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30152400-30160200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:30152400-30160200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:30152400-30160200	Strong transcription	Esophagus	oesophagus
47	chr6:30152400-30160200	Strong transcription	Lung	lung
48	chr6:30152400-30160200	Strong transcription	Spleen	Spleen
49	chr6:30152400-30160400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:30152400-30160400	Strong transcription	Placenta Amnion	Placenta Amnion

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