Variant report

Variant	rs1321505
Chromosome Location	chr6:28052823-28052824
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28049008..28053394-chr6:28054919..28058473,6	MCF-7	breast:
2	chr6:28047399..28050542-chr6:28051923..28057231,4	MCF-7	breast:
3	chr6:28047374..28049221-chr6:28051940..28054259,3	MCF-7	breast:
4	chr6:28050980..28053789-chr6:28055600..28058077,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272009	Chromatin interaction
ENSG00000197279	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10456362	0.93[CEU][hapmap]
rs11965538	0.93[CEU][hapmap]
rs12055625	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13200462	0.93[CEU][hapmap]
rs1321504	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13437126	1.00[ASN][1000 genomes]
rs13437444	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1419183	0.93[CEU][hapmap]
rs149943	1.00[CHB][hapmap]
rs149990	1.00[CHB][hapmap]
rs1679709	0.93[CEU][hapmap]
rs1679732	0.93[CEU][hapmap]
rs16893573	1.00[CHB][hapmap]
rs16893601	1.00[CHB][hapmap]
rs16893735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17720293	0.85[CEU][hapmap]
rs1778507	0.90[YRI][hapmap]
rs1778508	0.93[CEU][hapmap]
rs1778511	0.93[CEU][hapmap]
rs202906	1.00[CHB][hapmap]
rs2799077	0.93[CEU][hapmap]
rs2799079	0.93[CEU][hapmap]
rs34130214	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3757188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4713139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	0.93[CEU][hapmap]
rs6920512	0.81[YRI][hapmap]
rs735765	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180562	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295765	1.00[YRI][hapmap]
rs9348792	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9357064	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9366717	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9368560	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9368561	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380031	1.00[CHB][hapmap]
rs9380032	1.00[CHB][hapmap]
rs9380051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9380064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380069	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9393882	1.00[CHB][hapmap]
rs9393889	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9393902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9393908	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9461432	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461439	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9461446	1.00[YRI][hapmap]
rs9468271	0.80[CHB][hapmap]
rs9468287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468300	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468301	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9468321	0.90[YRI][hapmap]
rs9468322	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1321505	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1321505	AL022393.7	cis	Muscle Skeletal	GTEx
rs1321505	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1321505	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1321505		cis	Lymphoblastoid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049400-28053200	Weak transcription	Lung	lung
2	chr6:28049400-28053400	Weak transcription	Ovary	ovary
3	chr6:28049400-28055400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:28049400-28056600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:28049400-28056800	Weak transcription	Aorta	Aorta
6	chr6:28049600-28053200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:28049600-28053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:28049600-28053400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:28049600-28053400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28049600-28053400	Weak transcription	Fetal Stomach	stomach
11	chr6:28049600-28053400	Weak transcription	Gastric	stomach
12	chr6:28049600-28053400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:28049600-28053400	Weak transcription	Small Intestine	intestine
14	chr6:28049600-28053400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:28049600-28054200	Weak transcription	Thymus	Thymus
16	chr6:28049600-28054800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:28049600-28055000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:28049600-28055200	Weak transcription	Colonic Mucosa	Colon
19	chr6:28049600-28055400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:28049600-28055600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:28049600-28055600	Weak transcription	Fetal Kidney	kidney
22	chr6:28049600-28056000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:28049600-28056000	Weak transcription	Left Ventricle	heart
24	chr6:28049600-28056400	Weak transcription	Esophagus	oesophagus
25	chr6:28049600-28056400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:28049600-28056600	Weak transcription	Psoas Muscle	Psoas
27	chr6:28049600-28057000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:28049600-28058600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:28049600-28058600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
31	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:28049800-28053200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:28049800-28053200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:28049800-28053200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:28049800-28053200	Weak transcription	Primary B cells from cord blood	blood
36	chr6:28049800-28053200	Weak transcription	Liver	Liver
37	chr6:28049800-28053200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:28049800-28053400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:28049800-28053400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:28049800-28053400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:28049800-28053400	Weak transcription	Fetal Intestine Large	intestine
42	chr6:28049800-28053400	Weak transcription	Fetal Intestine Small	intestine
43	chr6:28049800-28053400	Weak transcription	Placenta	Placenta
44	chr6:28049800-28053600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:28049800-28055400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:28049800-28055400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:28049800-28055400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:28049800-28055400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:28049800-28055600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:28049800-28055600	Weak transcription	Stomach Mucosa	stomach

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