Variant report

Variant	rs6489247
Chromosome Location	chr12:123385443-123385444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123379396..123382383-chr12:123382549..123386101,3	MCF-7	breast:
2	chr12:123379239..123381321-chr12:123385286..123388225,2	K562	blood:
3	chr12:123378665..123382104-chr12:123382212..123387589,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10773627	0.83[CEU][hapmap]
rs12255	0.83[CEU][hapmap]
rs2061098	0.85[CHB][hapmap]
rs2061101	0.83[CHB][hapmap]
rs2135014	0.83[CEU][hapmap]
rs2271050	0.83[CEU][hapmap]
rs2292134	0.83[CEU][hapmap]
rs2292136	1.00[CEU][hapmap]
rs3852537	0.83[CEU][hapmap]
rs4759355	0.83[CEU][hapmap]
rs4759382	0.83[CEU][hapmap]
rs4759389	0.83[CEU][hapmap]
rs4759393	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs6489245	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs7138398	0.91[CEU][hapmap]
rs7139055	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs7294991	0.83[CEU][hapmap]
rs7306047	1.00[ASW][hapmap];0.80[YRI][hapmap]
rs7309225	0.83[CEU][hapmap]
rs7972447	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs897386	0.81[CEU][hapmap]
rs897391	0.83[CEU][hapmap]
rs897393	0.83[CEU][hapmap]
rs921808	0.83[CEU][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6489247	HIP1R	cis	parietal	SCAN
rs6489247	CCDC62	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123381000-123386000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:123381000-123387400	Weak transcription	Liver	Liver
3	chr12:123381000-123387400	Weak transcription	Fetal Heart	heart
4	chr12:123381000-123387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:123381200-123386000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:123381200-123386200	Weak transcription	Fetal Intestine Small	intestine
7	chr12:123381200-123387000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:123381200-123387400	Weak transcription	Fetal Brain Female	brain
9	chr12:123381200-123387600	Weak transcription	Fetal Intestine Large	intestine
10	chr12:123381200-123388400	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:123383200-123387000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:123383400-123386000	Weak transcription	K562	blood
13	chr12:123383400-123386400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:123383600-123386200	Enhancers	Primary B cells from cord blood	blood
15	chr12:123383600-123386200	Enhancers	Primary T cells from cord blood	blood
16	chr12:123383600-123387000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:123383600-123387400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:123383600-123387400	Weak transcription	A549	lung
19	chr12:123383600-123387800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:123383800-123386200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:123383800-123386600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:123383800-123386600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:123383800-123386600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:123383800-123386800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr12:123383800-123387000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr12:123383800-123387200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:123383800-123387600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:123383800-123387600	Weak transcription	Stomach Mucosa	stomach
29	chr12:123383800-123394600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:123384000-123386000	Enhancers	GM12878-XiMat	blood
31	chr12:123384000-123386600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:123384000-123387200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:123384000-123387400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:123384000-123387400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:123384000-123387800	Weak transcription	Brain Angular Gyrus	brain
36	chr12:123384400-123385800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:123384400-123386000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:123384400-123387200	Weak transcription	Colonic Mucosa	Colon
39	chr12:123384400-123387400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:123384600-123385600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:123384600-123386000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:123384600-123386000	Weak transcription	Dnd41	blood
43	chr12:123384600-123386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:123384800-123386000	Weak transcription	Placenta	Placenta
45	chr12:123384800-123387000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:123384800-123387800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:123384800-123387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:123384800-123387800	Weak transcription	Fetal Thymus	thymus
49	chr12:123384800-123387800	Weak transcription	Pancreas	Pancrea
50	chr12:123385000-123386200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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