Variant report

Variant	rs12900004
Chromosome Location	chr15:77844904-77844905
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	chr15:77842609..77845174-chr8:144895503..144897609,2	MCF-7	breast:
2	chr15:77840852..77845440-chr15:77846808..77850692,5	K562	blood:

Variant related genes	Relation type
ENSG00000180900	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1005752	0.86[JPT][hapmap]
rs11633054	0.86[JPT][hapmap]
rs11854328	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855188	0.95[EUR][1000 genomes]
rs11857450	0.86[JPT][hapmap]
rs11857860	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12324627	0.90[JPT][hapmap]
rs12901130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901503	0.86[JPT][hapmap]
rs12904553	0.83[ASN][1000 genomes]
rs12905285	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12907746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913899	0.81[ASN][1000 genomes]
rs2055901	0.86[JPT][hapmap]
rs4886869	0.86[JPT][hapmap]
rs4886873	0.84[CEU][hapmap]
rs4886875	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886876	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009090	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495240	1.00[JPT][hapmap]
rs7162637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170877	0.84[ASN][1000 genomes]
rs7178572	0.86[JPT][hapmap]
rs8034133	0.86[JPT][hapmap]
rs907369	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907372	0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs907388	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12900004	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
2	chr15:77836200-77846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:77838600-77849800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:77838800-77849000	Weak transcription	Gastric	stomach
5	chr15:77839800-77846400	Weak transcription	Fetal Heart	heart
6	chr15:77840600-77848600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:77840800-77845200	Enhancers	Placenta	Placenta
8	chr15:77841400-77846600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:77841600-77845400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:77841600-77845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:77841600-77846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:77841600-77846800	Weak transcription	Spleen	Spleen
13	chr15:77841600-77847000	Weak transcription	Fetal Brain Female	brain
14	chr15:77841600-77849600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:77842200-77850200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr15:77842800-77850400	Enhancers	Brain Hippocampus Middle	brain
17	chr15:77843000-77845000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr15:77843400-77846400	Weak transcription	Fetal Stomach	stomach
19	chr15:77843600-77846200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:77843800-77845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:77843800-77846000	Bivalent Enhancer	HepG2	liver
22	chr15:77843800-77847400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:77844000-77846000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:77844000-77846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:77844400-77845000	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:77844400-77845000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr15:77844400-77846600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr15:77844400-77848400	Weak transcription	Fetal Intestine Small	intestine
29	chr15:77844400-77850200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:77844600-77845200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:77844600-77845200	Enhancers	Brain Cingulate Gyrus	brain
32	chr15:77844600-77850000	Enhancers	Brain Anterior Caudate	brain
33	chr15:77844800-77845000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:77844800-77845000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr15:77844800-77845400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:77844800-77845600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:77844800-77848200	Enhancers	Brain Angular Gyrus	brain
38	chr15:77844800-77849800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:77844800-77849800	Enhancers	Brain Substantia Nigra	brain

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