Variant report

Variant	rs10876968
Chromosome Location	chr12:57644767-57644768
allele	G/T
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	POLR2A	chr12:57644734-57645125	K562	blood:	n/a	n/a
2	CTCF	chr12:57644740-57644890	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57640540..57643172-chr12:57644604..57647826,3	K562	blood:
2	chr12:57607877..57611743-chr12:57643490..57646687,3	K562	blood:

Variant related genes	Relation type
STAC3	TF binding region
ENSG00000182379	Chromatin interaction
ENSG00000185482	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10876971	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11172140	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11172155	0.83[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11830804	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12227309	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2943692	0.81[CEU][hapmap]
rs2943693	0.83[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs3204635	0.92[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs538548	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs567895	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7133572	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7302906	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7963352	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7966846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976512	0.86[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10876968	OR6C4	cis	parietal	SCAN
rs10876968	CDK4	cis	cerebellum	SCAN
rs10876968	APOF	cis	parietal	SCAN
rs10876968	SDR9C7	cis	cerebellum	SCAN
rs10876968	OR6C1	cis	parietal	SCAN
rs10876968	DNAJC14	cis	cerebellum	SCAN
rs10876968	CDKN2A	trans	lymphoblastoid	seeQTL
rs10876968	SP7	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57637200-57647400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:57637200-57648400	Weak transcription	Brain Angular Gyrus	brain
3	chr12:57637400-57647200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57637600-57644800	Weak transcription	NHLF	lung
5	chr12:57637600-57648400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:57637600-57648400	Weak transcription	Lung	lung
7	chr12:57637600-57649000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:57637600-57649600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:57637600-57651200	Weak transcription	NHDF-Ad	bronchial
10	chr12:57637600-57654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:57637800-57645800	Weak transcription	Osteobl	bone
12	chr12:57637800-57648400	Weak transcription	Spleen	Spleen
13	chr12:57637800-57649800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:57638000-57647000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:57638000-57647200	Weak transcription	Fetal Brain Female	brain
16	chr12:57638000-57648200	Weak transcription	Primary T cells from cord blood	blood
17	chr12:57638000-57648400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:57638000-57648400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:57638000-57648400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:57638000-57648400	Weak transcription	Brain Anterior Caudate	brain
21	chr12:57638000-57648400	Weak transcription	Pancreas	Pancrea
22	chr12:57638000-57649000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:57638000-57649000	Weak transcription	Dnd41	blood
24	chr12:57638000-57649400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:57638000-57649400	Weak transcription	Fetal Heart	heart
26	chr12:57638000-57649600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:57638000-57649600	Weak transcription	Right Ventricle	heart
28	chr12:57638000-57651200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:57638000-57651200	Weak transcription	Fetal Brain Male	brain
30	chr12:57638200-57648000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:57638200-57648400	Weak transcription	Colonic Mucosa	Colon
32	chr12:57638400-57648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:57638600-57649600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:57638800-57673600	Weak transcription	Stomach Mucosa	stomach
35	chr12:57639000-57647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:57639000-57647000	Weak transcription	Fetal Intestine Small	intestine
37	chr12:57639000-57648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:57639000-57648000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:57639200-57647200	Weak transcription	Fetal Stomach	stomach
40	chr12:57639200-57648200	Weak transcription	Brain Germinal Matrix	brain
41	chr12:57639200-57648400	Weak transcription	Liver	Liver
42	chr12:57639200-57648400	Weak transcription	Placenta	Placenta
43	chr12:57639200-57648600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:57639600-57649800	Weak transcription	A549	lung
45	chr12:57639600-57651200	Weak transcription	Hela-S3	cervix
46	chr12:57639600-57651200	Weak transcription	HepG2	liver
47	chr12:57640400-57645000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr12:57640600-57649200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:57640800-57646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:57641000-57649200	Weak transcription	Fetal Lung	lung

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