Variant report

Variant	rs1504978
Chromosome Location	chr5:118610560-118610561
allele	C/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:118606735..118608940-chr5:118610555..118612827,2	MCF-7	breast:
2	chr5:118406002..118408491-chr5:118610029..118612989,2	MCF-7	breast:
3	chr5:118609309..118611605-chr5:118653973..118656263,2	K562	blood:
4	chr5:118574634..118576211-chr5:118609734..118611582,2	MCF-7	breast:
5	chr5:118607071..118610754-chr5:118620607..118623123,4	K562	blood:
6	chr5:118602852..118606444-chr5:118607322..118611443,10	MCF-7	breast:
7	chr5:118608930..118611747-chr5:118623733..118626239,2	MCF-7	breast:
8	chr5:118608976..118610924-chr5:118611677..118614911,3	K562	blood:
9	chr5:118609964..118611606-chr5:118621803..118623586,2	MCF-7	breast:
10	chr5:118602128..118606181-chr5:118606426..118611824,11	MCF-7	breast:
11	chr5:118610421..118612422-chr5:118613685..118615437,2	MCF-7	breast:
12	chr5:118609066..118610745-chr5:118637168..118638991,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000249494	Chromatin interaction
ENSG00000145779	Chromatin interaction
ENSG00000172869	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1504977	0.91[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1024648	chr5:118608175-118678268	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3388576	chr5:118610398-118610749	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1504978	PRDM6	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118604800-118612000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr5:118605000-118611800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr5:118605400-118611200	Weak transcription	Lung	lung
4	chr5:118605400-118621000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:118605600-118611800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr5:118605600-118612800	Weak transcription	Fetal Kidney	kidney
7	chr5:118605600-118618200	Weak transcription	Fetal Stomach	stomach
8	chr5:118606200-118617600	Weak transcription	Fetal Lung	lung
9	chr5:118606600-118612000	Enhancers	Pancreas	Pancrea
10	chr5:118606800-118610600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr5:118606800-118610600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:118606800-118611200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr5:118606800-118611400	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:118606800-118612000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:118606800-118614600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:118607000-118610600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:118607000-118611200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr5:118607000-118612400	Enhancers	Small Intestine	intestine
19	chr5:118607200-118610600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:118607400-118612400	Enhancers	Placenta	Placenta
21	chr5:118607800-118610600	Genic enhancers	K562	blood
22	chr5:118607800-118611000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:118608400-118610600	Enhancers	Fetal Muscle Leg	muscle
24	chr5:118608400-118611200	Enhancers	A549	lung
25	chr5:118608400-118611800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:118608400-118611800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:118608800-118610600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:118608800-118610600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:118608800-118610600	Enhancers	Aorta	Aorta
30	chr5:118608800-118610600	Enhancers	HepG2	liver
31	chr5:118608800-118610800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:118608800-118610800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr5:118608800-118611000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:118608800-118611200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr5:118608800-118611200	Enhancers	Fetal Intestine Small	intestine
36	chr5:118608800-118612000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:118609000-118610600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr5:118609000-118610600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr5:118609000-118611200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr5:118609000-118611200	Enhancers	Esophagus	oesophagus
41	chr5:118609000-118611400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:118609000-118611400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:118609200-118611200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:118609200-118611400	Enhancers	Fetal Intestine Large	intestine
45	chr5:118609200-118612600	Enhancers	Duodenum Mucosa	Duodenum
46	chr5:118609400-118610600	Enhancers	Colonic Mucosa	Colon
47	chr5:118609400-118610600	Enhancers	Fetal Heart	heart
48	chr5:118609400-118610600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr5:118609400-118610800	Enhancers	Stomach Smooth Muscle	stomach
50	chr5:118609400-118611400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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