Variant report

Variant	rs388038
Chromosome Location	chr2:7139212-7139213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:7137807..7140160-chr2:7167317..7168870,2	K562	blood:
2	chr2:7130628..7133079-chr2:7138526..7140206,2	MCF-7	breast:
3	chr2:7134506..7138740-chr2:7139151..7141142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151692	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2444299	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460401	0.94[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs309309	0.94[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs309316	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309318	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309320	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309324	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs364891	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771997	0.81[MEX][hapmap]
rs397865	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407427	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407798	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs436955	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441766	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs443363	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs454213	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73141632	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs771273	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs388038	RNF144A	cis	cerebellum	SCAN
rs388038	RNF144A	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
2	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:7115800-7148800	Weak transcription	Esophagus	oesophagus
4	chr2:7121200-7145400	Weak transcription	Thymus	Thymus
5	chr2:7121400-7148200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:7126600-7147600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:7126800-7141800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:7126800-7148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:7127200-7154000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:7127600-7143600	Weak transcription	HepG2	liver
12	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:7131200-7141000	Strong transcription	Primary T cells from cord blood	blood
14	chr2:7131200-7146800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:7131400-7150200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:7131400-7162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:7131600-7154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:7131600-7154200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:7132800-7146600	Weak transcription	Fetal Heart	heart
20	chr2:7133400-7147400	Weak transcription	Fetal Kidney	kidney
21	chr2:7133800-7147400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:7133800-7147600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:7133800-7147800	Weak transcription	Fetal Brain Female	brain
24	chr2:7133800-7150800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:7134400-7140800	Strong transcription	Dnd41	blood
26	chr2:7134400-7147400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:7135000-7146800	Weak transcription	Lung	lung
28	chr2:7135200-7145400	Weak transcription	Fetal Brain Male	brain
29	chr2:7135400-7139400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:7135400-7139400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:7135400-7145000	Weak transcription	Brain Germinal Matrix	brain
32	chr2:7135600-7139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:7135800-7146800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:7136000-7139400	Weak transcription	Left Ventricle	heart
35	chr2:7137200-7140000	Weak transcription	Fetal Stomach	stomach
36	chr2:7137200-7146200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:7137200-7149800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:7137400-7160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:7137600-7142400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:7137800-7144400	Weak transcription	Adipose Nuclei	Adipose
41	chr2:7138000-7140000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:7138000-7140200	Enhancers	Brain Anterior Caudate	brain
43	chr2:7138000-7147000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:7138400-7139400	Enhancers	Fetal Lung	lung
45	chr2:7138400-7139600	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:7138400-7140200	Enhancers	Brain Substantia Nigra	brain
47	chr2:7138400-7140200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:7138400-7140400	Enhancers	Brain Angular Gyrus	brain
49	chr2:7138400-7140400	Enhancers	Brain Hippocampus Middle	brain
50	chr2:7138400-7140800	Enhancers	Skeletal Muscle Female	skeletal muscle

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