Variant report

Variant	rs6488868
Chromosome Location	chr12:123799974-123799975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123754997..123757779-chr12:123799876..123802346,2	MCF-7	breast:
2	chr12:123779615..123782241-chr12:123799621..123801825,2	K562	blood:
3	chr12:123797348..123800081-chr12:123802978..123805835,2	K562	blood:
4	chr12:123798241..123802098-chr12:123803034..123805824,3	K562	blood:
5	chr12:123779615..123782241-chr12:123799621..123802111,3	K562	blood:
6	chr12:123798336..123800594-chr12:123811189..123813039,2	MCF-7	breast:
7	chr12:123792059..123795605-chr12:123796583..123800633,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10083067	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10444447	0.82[ASN][1000 genomes]
rs10444448	0.82[ASN][1000 genomes]
rs10773000	0.90[GIH][hapmap]
rs10773007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10773009	1.00[ASN][1000 genomes]
rs10773010	1.00[ASN][1000 genomes]
rs10773014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10846489	0.87[GIH][hapmap]
rs10846495	0.82[ASN][1000 genomes]
rs10846496	0.82[ASN][1000 genomes]
rs10846498	0.82[ASN][1000 genomes]
rs10846499	0.82[ASN][1000 genomes]
rs10846500	0.82[ASN][1000 genomes]
rs10846501	0.82[ASN][1000 genomes]
rs10846503	0.91[ASN][1000 genomes]
rs10846504	0.91[ASN][1000 genomes]
rs10846509	1.00[ASN][1000 genomes]
rs10846510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846511	1.00[ASN][1000 genomes]
rs10846514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846518	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846521	1.00[ASN][1000 genomes]
rs10846522	1.00[ASN][1000 genomes]
rs10846524	1.00[ASN][1000 genomes]
rs11057231	0.82[ASN][1000 genomes]
rs11057240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11057243	0.91[ASN][1000 genomes]
rs11057250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11057251	0.92[GIH][hapmap]
rs11057254	0.82[EUR][1000 genomes]
rs11057261	0.82[EUR][1000 genomes]
rs11057264	1.00[ASN][1000 genomes]
rs11057266	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11057276	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs11057285	1.00[ASN][1000 genomes]
rs11057286	1.00[ASN][1000 genomes]
rs1109559	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs11608305	0.84[CEU][hapmap]
rs12298826	0.88[ASW][hapmap]
rs12304248	0.80[YRI][hapmap]
rs12316131	0.88[ASW][hapmap]
rs12322888	0.93[ASW][hapmap]
rs12371973	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1568428	0.87[GIH][hapmap]
rs1662	0.82[CHB][hapmap]
rs1727295	0.82[CEU][hapmap]
rs1879379	0.87[GIH][hapmap]
rs28376696	0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28397122	1.00[ASN][1000 genomes]
rs28406193	0.88[ASW][hapmap]
rs28419092	0.81[EUR][1000 genomes]
rs28454135	1.00[ASN][1000 genomes]
rs28458312	0.88[ASW][hapmap]
rs28472704	0.82[ASW][hapmap]
rs28475177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28533432	0.81[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs28573826	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28633324	1.00[ASN][1000 genomes]
rs28636834	0.88[ASW][hapmap]
rs28646185	0.91[ASN][1000 genomes]
rs28655516	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28660661	1.00[ASN][1000 genomes]
rs28713448	0.82[CHB][hapmap]
rs28861152	1.00[ASN][1000 genomes]
rs28898283	1.00[ASN][1000 genomes]
rs4281511	0.91[ASN][1000 genomes]
rs4313613	0.91[ASN][1000 genomes]
rs61388686	0.82[EUR][1000 genomes]
rs61953413	0.82[ASN][1000 genomes]
rs61955088	1.00[ASN][1000 genomes]
rs61955089	0.91[ASN][1000 genomes]
rs61955114	0.91[ASN][1000 genomes]
rs61955117	1.00[ASN][1000 genomes]
rs73231946	0.82[ASN][1000 genomes]
rs9668827	0.89[YRI][hapmap]

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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6488868	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs6488868	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs6488868	HNF1A	cis	cerebellum	SCAN
rs6488868	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs6488868	TMEM120B	cis	parietal	SCAN
rs6488868	COQ5	cis	parietal	SCAN
rs6488868	SBNO1,LOC728046	cis	brain	BrainEAC
rs6488868	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs6488868	PITPNM2	cis	cerebellum	SCAN
rs6488868	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs6488868	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs6488868	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs6488868	ANAPC5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123772800-123821000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:123773000-123835200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:123773200-123830600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:123773200-123834200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:123773200-123835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:123773200-123835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:123773400-123811600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:123773400-123812400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:123773400-123826200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:123773400-123826200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:123773400-123826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:123773400-123835000	Strong transcription	Fetal Thymus	thymus
15	chr12:123773400-123835400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:123773600-123816000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:123773600-123830800	Strong transcription	Placenta	Placenta
19	chr12:123773600-123835200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:123773600-123835400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:123773800-123826200	Strong transcription	Adipose Nuclei	Adipose
22	chr12:123773800-123826200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr12:123773800-123834800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:123774000-123802800	Strong transcription	Osteobl	bone
27	chr12:123774000-123820600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:123774000-123821600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:123774000-123835000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:123774000-123835200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:123774000-123835400	Strong transcription	Dnd41	blood
32	chr12:123774400-123821200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:123774600-123822200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:123775600-123812200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123775600-123835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:123775800-123821000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:123776200-123804000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:123776200-123826000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:123776200-123830600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:123776400-123835000	Strong transcription	Thymus	Thymus
41	chr12:123776600-123834400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:123777000-123835400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:123777600-123834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:123778600-123816200	Strong transcription	A549	lung
45	chr12:123778800-123822600	Strong transcription	Liver	Liver
46	chr12:123779800-123814800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:123780000-123830600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:123781800-123806800	Strong transcription	GM12878-XiMat	blood
49	chr12:123782600-123804400	Weak transcription	Fetal Heart	heart
50	chr12:123784200-123805000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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