Variant report

Variant	rs2378400
Chromosome Location	chr1:220799213-220799214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:220799064-220799345	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
HDAC1P2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10495149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10746403	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779412	1.00[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779413	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779414	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863561	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11118567	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11118570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11118573	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11118576	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118579	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118588	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588721	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1193032	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044432	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126252	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12408540	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12735691	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1933001	0.83[AMR][1000 genomes]
rs2152836	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244448	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2589581	0.86[ASN][1000 genomes]
rs2589586	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2589589	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2786606	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2786610	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2786617	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2889895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3753873	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs3753874	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs3767319	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3767320	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767321	1.00[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3899315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3905814	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4120669	0.81[CHB][hapmap]
rs4338357	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846326	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes]
rs4846327	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4846655	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541154	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6675368	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs6695583	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514431	0.80[CEU][hapmap]
rs9430949	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220752600-220808600	Weak transcription	Left Ventricle	heart
2	chr1:220767800-220826400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:220768000-220804600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:220768000-220813800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:220778800-220837200	Weak transcription	NHEK	skin
6	chr1:220782800-220825800	Weak transcription	Fetal Brain Male	brain
7	chr1:220783200-220815000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:220784200-220836600	Weak transcription	Fetal Lung	lung
9	chr1:220784800-220815000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:220785000-220815400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:220785800-220808600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:220786800-220799800	Weak transcription	Fetal Heart	heart
13	chr1:220791000-220804200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:220791200-220828600	Weak transcription	Right Ventricle	heart
15	chr1:220791200-220841200	Weak transcription	HMEC	breast
16	chr1:220791400-220801600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:220792000-220834200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:220792800-220803600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:220795600-220801000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:220795800-220802000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:220796200-220827800	Weak transcription	Gastric	stomach
22	chr1:220796800-220799600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:220797200-220801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:220798000-220836400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:220798200-220801000	Strong transcription	Brain Germinal Matrix	brain
26	chr1:220798600-220799600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:220798600-220800400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:220798600-220800400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:220798800-220799600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:220798800-220800600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:220798800-220800800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:220798800-220826200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:220799000-220799800	Strong transcription	Aorta	Aorta
34	chr1:220799000-220800000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:220799000-220800000	Strong transcription	Adipose Nuclei	Adipose
36	chr1:220799000-220800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:220799000-220800200	Strong transcription	Fetal Stomach	stomach
38	chr1:220799000-220800400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:220799000-220800600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:220799200-220799800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:220799200-220799800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:220799200-220800000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:220799200-220800000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:220799200-220800000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:220799200-220800000	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:220799200-220801400	Strong transcription	Fetal Brain Female	brain

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