Variant report

Variant	rs2232438
Chromosome Location	chr6:28350479-28350480
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28302793..28305456-chr6:28347856..28351806,3	MCF-7	breast:
2	chr6:28302573..28306599-chr6:28349951..28354470,6	K562	blood:
3	chr6:28316530..28318158-chr6:28350135..28352700,2	K562	blood:
4	chr6:28336816..28339223-chr6:28349568..28351639,2	MCF-7	breast:
5	chr6:27858275..27861219-chr6:28349730..28352798,3	MCF-7	breast:
6	chr6:28302507..28305351-chr6:28350132..28351669,2	K562	blood:
7	chr6:28189695..28192033-chr6:28349571..28352462,4	K562	blood:
8	chr6:28098221..28099883-chr6:28348918..28351398,2	MCF-7	breast:
9	chr6:28187278..28189645-chr6:28349848..28351599,2	K562	blood:
10	chr6:28189695..28193201-chr6:28349960..28353387,4	K562	blood:
11	chr6:28346545..28348363-chr6:28349584..28351262,2	MCF-7	breast:
12	chr6:28349465..28351465-chr6:28394048..28396108,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10484540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10484541	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1555046	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1556957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894121	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17313059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17313276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17314224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17314865	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17314991	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17315340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17315648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17315739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17316033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17392982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393066	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17393342	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393786	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17720687	0.85[CEU][hapmap]
rs2027362	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213230	0.88[CHB][hapmap]
rs213231	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs2232419	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2232434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56001748	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56241479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56787378	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57126418	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57204212	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57366176	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59732975	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60184496	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60660967	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6915122	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73740609	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73740620	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73740622	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73740623	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7774788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468378	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9717944	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2232438	ZSCAN12	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
7	chr6:28333800-28350800	Weak transcription	Lung	lung
8	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
10	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:28334200-28351000	Weak transcription	Gastric	stomach
12	chr6:28334200-28351200	Weak transcription	Spleen	Spleen
13	chr6:28334400-28350600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:28334400-28351000	Weak transcription	Esophagus	oesophagus
15	chr6:28334600-28351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:28344800-28350800	Weak transcription	Small Intestine	intestine
17	chr6:28345000-28361600	Strong transcription	Dnd41	blood
18	chr6:28345600-28350600	Strong transcription	Brain Germinal Matrix	brain
19	chr6:28346200-28350600	Weak transcription	Fetal Stomach	stomach
20	chr6:28347200-28350600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:28347200-28350800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:28347400-28350600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr6:28347600-28350600	Strong transcription	Primary T cells from cord blood	blood
24	chr6:28348000-28350600	Genic enhancers	HepG2	liver
25	chr6:28348200-28350600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:28348400-28350800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:28348400-28351000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:28348400-28357800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:28348600-28350600	Weak transcription	Adipose Nuclei	Adipose
30	chr6:28348600-28350600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:28348600-28350800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:28348600-28350800	Weak transcription	Fetal Brain Male	brain
33	chr6:28348600-28350800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:28348600-28350800	Weak transcription	NHDF-Ad	bronchial
35	chr6:28348600-28351000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:28348600-28351000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:28348800-28350600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:28348800-28350600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:28348800-28350600	Weak transcription	HUVEC	blood vessel
40	chr6:28348800-28350800	Weak transcription	Brain Angular Gyrus	brain
41	chr6:28348800-28350800	Weak transcription	Brain Substantia Nigra	brain
42	chr6:28348800-28350800	Weak transcription	Thymus	Thymus
43	chr6:28348800-28351000	Weak transcription	Placenta	Placenta
44	chr6:28349000-28350600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:28349400-28350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:28349400-28350600	Enhancers	Fetal Heart	heart
47	chr6:28349400-28350800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:28349800-28350600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr6:28349800-28350800	Enhancers	Colon Smooth Muscle	Colon
50	chr6:28350000-28350600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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