Variant report

Variant	rs10876862
Chromosome Location	chr12:56318043-56318044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:56317946-56318064	SH-SY5Y	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56318003..56321783-chr12:56433300..56437111,4	K562	blood:
2	chr12:56317848..56319643-chr12:56515602..56517864,2	K562	blood:
3	chr12:56224798..56227031-chr12:56316419..56319091,2	K562	blood:
4	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
5	chr12:56232360..56237326-chr12:56316163..56320896,5	K562	blood:
6	chr12:56307549..56310271-chr12:56316708..56318919,2	MCF-7	breast:
7	chr12:56317383..56319577-chr12:56434769..56436462,2	MCF-7	breast:

No data

Variant related genes	Relation type
DGKA	TF binding region
ENSG00000135392	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000123342	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10128982	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1052206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747760	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783774	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783775	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1136082	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12298127	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1681070	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1681071	0.82[YRI][hapmap]
rs1681080	0.82[YRI][hapmap]
rs1689509	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs1701698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1701699	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2101718	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2640568	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs4414258	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61956428	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581087	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705697	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs705711	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135133	0.81[EUR][1000 genomes]
rs7297871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312870	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs772462	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772464	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs772468	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs772470	0.82[YRI][hapmap]
rs772473	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs772475	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.80[ASN][1000 genomes]
rs772697	0.82[YRI][hapmap]
rs772700	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs772704	0.94[CEU][hapmap]
rs9739192	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9739196	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10876862	GLS2	cis	cerebellum	SCAN
rs10876862	LARP4	cis	parietal	SCAN
rs10876862	SDR9C7	cis	cerebellum	SCAN
rs10876862	RBMS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56285200-56320000	Weak transcription	Pancreas	Pancrea
3	chr12:56291400-56319000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56293600-56319200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:56293800-56319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:56294200-56319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:56294400-56319600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:56296000-56319600	Weak transcription	Right Ventricle	heart
9	chr12:56296200-56319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:56296800-56319600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:56297200-56319200	Weak transcription	Colonic Mucosa	Colon
12	chr12:56297200-56319600	Weak transcription	Brain Germinal Matrix	brain
13	chr12:56297200-56319600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:56297200-56320000	Weak transcription	Gastric	stomach
15	chr12:56297200-56320000	Weak transcription	Spleen	Spleen
16	chr12:56297600-56319600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:56300400-56319400	Weak transcription	HSMMtube	muscle
18	chr12:56303400-56319600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:56303600-56319600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:56303800-56319400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:56303800-56319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:56303800-56319600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:56304000-56319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:56307400-56319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:56307600-56319600	Weak transcription	Fetal Kidney	kidney
26	chr12:56308000-56319600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:56308200-56319400	Weak transcription	HSMM	muscle
28	chr12:56308400-56319200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:56308800-56318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:56308800-56320000	Weak transcription	Small Intestine	intestine
31	chr12:56309200-56319600	Weak transcription	HUVEC	blood vessel
32	chr12:56309400-56320000	Weak transcription	Stomach Mucosa	stomach
33	chr12:56309600-56319600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:56310000-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:56310200-56319600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:56310400-56318800	Weak transcription	HMEC	breast
37	chr12:56310400-56319400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:56310800-56319000	Weak transcription	K562	blood
39	chr12:56310800-56319200	Weak transcription	Fetal Lung	lung
40	chr12:56310800-56320000	Weak transcription	Esophagus	oesophagus
41	chr12:56312400-56319400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:56312800-56319200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:56313000-56319000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:56313200-56319200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:56313200-56319400	Weak transcription	NHLF	lung
46	chr12:56313400-56318800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:56313800-56318600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:56313800-56319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:56313800-56320200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:56314200-56318200	Strong transcription	Monocytes-CD14+_RO01746	blood

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