Variant report

Variant	rs28378998
Chromosome Location	chr12:122026527-122026528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122017945..122023539-chr12:122025012..122028731,5	K562	blood:

Variant related genes	Relation type
ENSG00000256742	Chromatin interaction
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12313273	0.87[MEX][hapmap]
rs28397246	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28489288	0.84[AMR][1000 genomes]
rs28508138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28517331	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28546504	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28552516	0.82[AMR][1000 genomes]
rs28594507	0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs28637676	0.88[YRI][hapmap]
rs3741595	0.92[MEX][hapmap];0.81[TSI][hapmap]
rs6486795	0.87[MEX][hapmap]
rs7313601	0.95[MEX][hapmap]
rs73227906	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73227912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28378998	SRRM4	cis	cerebellum	SCAN
rs28378998	GTF2H3	cis	cerebellum	SCAN
rs28378998	NME2P1	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122020200-122027800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:122020600-122027800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:122020600-122028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:122020600-122030200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:122020800-122026800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:122020800-122027600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:122020800-122027600	Weak transcription	Psoas Muscle	Psoas
8	chr12:122020800-122027600	Weak transcription	Right Atrium	heart
9	chr12:122020800-122027800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:122020800-122040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:122021000-122027200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:122021000-122027600	Weak transcription	Placenta	Placenta
13	chr12:122021000-122027800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:122021000-122027800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:122021000-122027800	Weak transcription	Fetal Stomach	stomach
16	chr12:122021000-122027800	Weak transcription	NHDF-Ad	bronchial
17	chr12:122021200-122027200	Weak transcription	Fetal Thymus	thymus
18	chr12:122021200-122027600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:122021200-122027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:122021200-122027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:122021200-122027800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:122021200-122027800	Weak transcription	Osteobl	bone
23	chr12:122021200-122028200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:122021200-122028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:122021200-122028400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:122021200-122028400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:122021200-122028400	Weak transcription	Aorta	Aorta
28	chr12:122021200-122036000	Weak transcription	Brain Germinal Matrix	brain
29	chr12:122021400-122027800	Weak transcription	HepG2	liver
30	chr12:122021600-122033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:122021800-122027400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:122022000-122028400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:122022200-122027400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:122022200-122027600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:122022200-122027600	Weak transcription	K562	blood
36	chr12:122022200-122027800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:122022200-122028200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:122022200-122028200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:122022200-122028400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:122022200-122028400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:122022200-122028600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:122022400-122028400	Weak transcription	Fetal Heart	heart
43	chr12:122022600-122027400	Weak transcription	Dnd41	blood
44	chr12:122024000-122028400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:122024200-122026800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:122024200-122027000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:122024200-122027200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:122024200-122027200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:122024200-122027400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:122024200-122028200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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