Variant report

Variant	rs2531825
Chromosome Location	chr6:28349264-28349265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28302793..28305456-chr6:28347856..28351806,3	MCF-7	breast:
2	chr6:28342156..28344769-chr6:28347005..28349721,3	MCF-7	breast:
3	chr6:28098221..28099883-chr6:28348918..28351398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005125	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052215	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10946954	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1124132	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1150705	0.81[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1150716	0.84[EUR][1000 genomes]
rs12214383	0.81[CEU][hapmap]
rs1233713	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13408	0.81[CEU][hapmap]
rs1361387	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1531681	0.81[CEU][hapmap]
rs1736891	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs1736895	0.81[CEU][hapmap]
rs2023493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108927	0.80[EUR][1000 genomes]
rs213228	0.84[MKK][hapmap];0.83[YRI][hapmap]
rs213232	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213237	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213238	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2142730	0.92[CEU][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes]
rs2247002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531803	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2531806	0.81[AMR][1000 genomes]
rs2531831	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531832	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2859348	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs2859365	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4455662	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6938371	0.81[YRI][hapmap]
rs7206	0.92[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs728122	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853684	0.92[CEU][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs916403	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs9368565	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468372	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs2531825	ZKSCAN3	cis	parietal	SCAN
rs2531825	ZKSCAN3	cis	cerebellum	SCAN
rs2531825	AL022393.7	cis	lung	GTEx
rs2531825	ZNF323	cis	Frontal Cortex	GTEx
rs2531825	NKAPL	cis	parietal	SCAN
rs2531825	ZSCAN23	cis	lung	GTEx
rs2531825	ZSCAN23	cis	lymphoblastoid	seeQTL
rs2531825	ZSCAN23	cis	Artery Tibial	GTEx
rs2531825	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2531825	ZNF187	cis	cerebellum	SCAN
rs2531825	AL022393.7	cis	Artery Aorta	GTEx
rs2531825	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs2531825	ZSCAN23	cis	Muscle Skeletal	GTEx
rs2531825	AL022393.7	cis	Artery Tibial	GTEx
rs2531825	HIST1H2BL	cis	cerebellum	SCAN
rs2531825	ZSCAN23	cis	Stomach	GTEx
rs2531825	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2531825	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2531825	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2531825	ZSCAN23	cis	cerebellum	SCAN
rs2531825	ZSCAN31	cis	lung	GTEx
rs2531825	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs2531825	AL022393.7	cis	Muscle Skeletal	GTEx
rs2531825	ZNF323	cis	parietal	SCAN
rs2531825	RP5-874C20.3	cis	Thyroid	GTEx
rs2531825	ZSCAN31	cis	Thyroid	GTEx
rs2531825	ZSCAN31	cis	Muscle Skeletal	GTEx
rs2531825	ZNF192	cis	cerebellum	SCAN
rs2531825	AL022393.7	cis	Nerve Tibial	GTEx
rs2531825	ZNF323	cis	cerebellum	SCAN
rs2531825	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2531825	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2531825	ZSCAN23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:28324600-28349600	Weak transcription	NHEK	skin
6	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
9	chr6:28333800-28349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:28333800-28349800	Weak transcription	Pancreas	Pancrea
11	chr6:28333800-28350800	Weak transcription	Lung	lung
12	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:28334000-28350000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
15	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:28334200-28349400	Weak transcription	Right Ventricle	heart
17	chr6:28334200-28349800	Weak transcription	Aorta	Aorta
18	chr6:28334200-28351000	Weak transcription	Gastric	stomach
19	chr6:28334200-28351200	Weak transcription	Spleen	Spleen
20	chr6:28334400-28350600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:28334400-28351000	Weak transcription	Esophagus	oesophagus
22	chr6:28334600-28351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:28344800-28350800	Weak transcription	Small Intestine	intestine
24	chr6:28345000-28350200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:28345000-28361600	Strong transcription	Dnd41	blood
26	chr6:28345200-28350200	Weak transcription	Hela-S3	cervix
27	chr6:28345600-28349400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28345600-28350000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28345600-28350000	Strong transcription	Fetal Intestine Large	intestine
30	chr6:28345600-28350000	Strong transcription	NH-A	brain
31	chr6:28345600-28350200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:28345600-28350200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:28345600-28350200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:28345600-28350200	Strong transcription	Fetal Thymus	thymus
35	chr6:28345600-28350600	Strong transcription	Brain Germinal Matrix	brain
36	chr6:28345800-28350400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:28346000-28350000	Strong transcription	HMEC	breast
38	chr6:28346000-28350200	ZNF genes & repeats	K562	blood
39	chr6:28346000-28350400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr6:28346200-28350000	Weak transcription	Fetal Intestine Small	intestine
41	chr6:28346200-28350200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:28346200-28350600	Weak transcription	Fetal Stomach	stomach
43	chr6:28346600-28349600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:28346600-28350000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr6:28346800-28350000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:28346800-28350200	Strong transcription	Fetal Lung	lung
47	chr6:28346800-28350400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:28346800-28350400	Strong transcription	Fetal Kidney	kidney
49	chr6:28347000-28350000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:28347200-28350200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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