Variant report

Variant	rs56241479
Chromosome Location	chr6:28389174-28389175
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28356707..28359445-chr6:28388134..28391982,4	K562	blood:
2	chr6:28356866..28359445-chr6:28388346..28391982,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1015690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484541	0.81[EUR][1000 genomes]
rs1555046	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1555047	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1556957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16894121	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17313059	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17313276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17314224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17314865	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17314991	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17315340	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17315648	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17315739	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17316033	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17392982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393066	0.81[EUR][1000 genomes]
rs17393342	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17393506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17393786	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027362	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2232419	0.81[EUR][1000 genomes]
rs2232434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2232438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56001748	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56787378	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57126418	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57204212	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57366176	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59732975	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60184496	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60660967	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915122	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740609	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73740620	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740622	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740623	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs758396	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774788	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468378	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9717944	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56241479	ZSCAN12	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28377600-28390200	Weak transcription	Fetal Lung	lung
3	chr6:28379400-28389200	Weak transcription	HSMM	muscle
4	chr6:28380800-28390600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:28381400-28390000	Weak transcription	Fetal Brain Female	brain
6	chr6:28383400-28390600	Weak transcription	Fetal Stomach	stomach
7	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
8	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:28384600-28390200	Weak transcription	NH-A	brain
10	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:28384800-28390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:28385000-28390600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28385200-28390600	Weak transcription	Placenta	Placenta
14	chr6:28385400-28391000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:28385400-28391200	Weak transcription	HSMMtube	muscle
16	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
17	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:28385600-28390800	Weak transcription	Aorta	Aorta
19	chr6:28385600-28390800	Weak transcription	Ovary	ovary
20	chr6:28385600-28410800	Weak transcription	Lung	lung
21	chr6:28385800-28390800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:28386000-28402200	Weak transcription	Osteobl	bone
24	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:28386200-28390000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:28386200-28390600	Weak transcription	Right Ventricle	heart
27	chr6:28386200-28391000	Weak transcription	Psoas Muscle	Psoas
28	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:28386600-28391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:28386600-28392200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:28386800-28392000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
35	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:28387400-28390600	Weak transcription	Fetal Intestine Large	intestine
37	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28387800-28390600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:28387800-28390600	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:28387800-28390800	Weak transcription	Brain Anterior Caudate	brain
42	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
43	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
45	chr6:28388000-28389800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:28388000-28390000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
49	chr6:28388400-28390600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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