Variant report

Variant	rs7966607
Chromosome Location	chr12:123373586-123373587
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123371782..123374478-chr12:123385509..123387711,2	K562	blood:
2	chr12:123317720..123322313-chr12:123372173..123377754,7	MCF-7	breast:
3	chr12:123371833..123374158-chr12:123459518..123462902,4	K562	blood:
4	chr12:123371397..123374446-chr12:123429800..123431973,3	MCF-7	breast:
5	chr12:123354952..123357571-chr12:123370695..123373701,5	MCF-7	breast:
6	chr12:123373192..123374846-chr12:123449556..123451152,2	MCF-7	breast:
7	chr12:123353502..123357222-chr12:123371821..123375830,5	MCF-7	breast:
8	chr12:123361905..123363893-chr12:123371746..123374359,2	MCF-7	breast:
9	chr12:123372928..123374670-chr12:123434344..123437637,4	MCF-7	breast:
10	chr12:123373155..123374696-chr12:123457739..123460648,2	MCF-7	breast:
11	chr12:123276806..123278323-chr12:123371531..123373689,2	MCF-7	breast:
12	chr12:123348287..123350765-chr12:123373068..123375043,2	MCF-7	breast:
13	chr12:123321572..123324516-chr12:123371831..123374446,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256028	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10847910	0.83[YRI][hapmap]
rs1671680	0.91[ASW][hapmap];0.88[LWK][hapmap];1.00[AMR][1000 genomes]
rs1696324	1.00[AMR][1000 genomes]
rs1798568	1.00[AMR][1000 genomes]
rs59499651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489246	0.87[AMR][1000 genomes]
rs7138206	1.00[AMR][1000 genomes]
rs7304234	0.85[AMR][1000 genomes]
rs7312620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7314233	0.85[AMR][1000 genomes]
rs7956122	0.92[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7966607	HIP1R	cis	lymphoblastoid	seeQTL
rs7966607	VPS37B	cis	lymphoblastoid	seeQTL
rs7966607	ABCB9	cis	lymphoblastoid	seeQTL
rs7966607	VPS37B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123366200-123379800	Weak transcription	Ovary	ovary
2	chr12:123367800-123375800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:123368600-123375600	Enhancers	NHDF-Ad	bronchial
4	chr12:123370400-123379400	Enhancers	Small Intestine	intestine
5	chr12:123370600-123374600	Enhancers	Pancreas	Pancrea
6	chr12:123370600-123375400	Enhancers	Spleen	Spleen
7	chr12:123370600-123377400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:123370600-123377600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr12:123370800-123374600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:123370800-123374600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:123370800-123375200	Enhancers	Lung	lung
12	chr12:123370800-123375400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:123370800-123375800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:123370800-123375800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:123370800-123378000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:123371000-123374000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:123371000-123375800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:123371200-123373600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:123371200-123374000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr12:123371400-123373800	Flanking Active TSS	A549	lung
21	chr12:123371400-123374000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr12:123371400-123375200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:123371400-123375400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:123371400-123375400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr12:123371400-123375800	Enhancers	NHLF	lung
26	chr12:123371400-123376400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:123371600-123373800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:123371600-123373800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:123371600-123374000	Flanking Active TSS	GM12878-XiMat	blood
30	chr12:123371600-123374800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr12:123371600-123380000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr12:123371800-123374000	Enhancers	Psoas Muscle	Psoas
33	chr12:123371800-123374000	Flanking Active TSS	Dnd41	blood
34	chr12:123371800-123374600	Enhancers	Brain Angular Gyrus	brain
35	chr12:123371800-123374800	Enhancers	Fetal Brain Male	brain
36	chr12:123371800-123376200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr12:123371800-123376200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:123371800-123378400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr12:123372000-123373800	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr12:123372000-123374000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:123372000-123374000	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:123372000-123375800	Enhancers	Brain Germinal Matrix	brain
43	chr12:123372200-123374000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:123372200-123374600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr12:123372200-123378400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:123372400-123373600	Active TSS	Esophagus	oesophagus
47	chr12:123372400-123373800	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr12:123372400-123373800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr12:123372400-123373800	Flanking Active TSS	Fetal Thymus	thymus
50	chr12:123372400-123373800	Flanking Active TSS	Thymus	Thymus

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