Variant report

Variant	rs17004573
Chromosome Location	chr21:44938155-44938156
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44839515..44855046-chr21:44918803..44938582,70	MCF-7	breast:
2	chr21:44936672..44939278-chr21:45002074..45004794,2	MCF-7	breast:
3	chr21:44935745..44939889-chr21:44996444..44998643,4	MCF-7	breast:
4	chr21:44933239..44939119-chr21:45027942..45032046,11	MCF-7	breast:
5	chr21:44936778..44938519-chr21:44970859..44973730,2	MCF-7	breast:
6	chr21:44934396..44939488-chr21:45063795..45068503,7	MCF-7	breast:
7	chr21:44727065..44728697-chr21:44937489..44939216,2	MCF-7	breast:
8	chr21:44936168..44938346-chr5:25477509..25479943,2	MCF-7	breast:
9	chr21:44935247..44938888-chr21:45036868..45039173,3	MCF-7	breast:
10	chr21:44759707..44762996-chr21:44935896..44938308,3	MCF-7	breast:
11	chr21:44752067..44754394-chr21:44936945..44938749,2	MCF-7	breast:
12	chr21:44935195..44942837-chr21:45027341..45034401,13	MCF-7	breast:
13	chr21:44935152..44938727-chr21:45130277..45133903,3	MCF-7	breast:
14	chr21:44936296..44939345-chr21:45062332..45065604,3	MCF-7	breast:
15	chr21:44936721..44939320-chr21:45041699..45043482,2	MCF-7	breast:
16	chr21:44844533..44847872-chr21:44929082..44940063,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000214326	Chromatin interaction
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17004541	1.00[CEU][hapmap]
rs17004576	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs17004583	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs17004591	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17004598	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2838332	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs8128469	1.00[CHB][hapmap]
rs8128769	1.00[CHB][hapmap]
rs8134178	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs9637200	0.82[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
5	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv587689	chr21:44884252-44986050	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1059264	chr21:44895863-44944515	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
10	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
13	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17004573	COL18A1	cis	cerebellum	SCAN
rs17004573	FAM3B	cis	parietal	SCAN
rs17004573	NDUFV3	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44926800-44938200	Enhancers	Fetal Thymus	thymus
2	chr21:44928800-44941000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr21:44929200-44938200	Enhancers	HSMM	muscle
4	chr21:44929200-44943400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr21:44929600-44943400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr21:44929800-44938600	Enhancers	Esophagus	oesophagus
7	chr21:44929800-44938800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:44929800-44943600	Enhancers	HMEC	breast
9	chr21:44930200-44938400	Enhancers	Pancreas	Pancrea
10	chr21:44930200-44939000	Enhancers	Fetal Intestine Small	intestine
11	chr21:44930600-44939800	Enhancers	Fetal Intestine Large	intestine
12	chr21:44933400-44938200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr21:44934000-44938400	Enhancers	Adipose Nuclei	Adipose
14	chr21:44934000-44938400	Enhancers	Left Ventricle	heart
15	chr21:44934000-44938400	Enhancers	Lung	lung
16	chr21:44934400-44938200	Enhancers	NH-A	brain
17	chr21:44934400-44938400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr21:44934400-44941200	Enhancers	HUVEC	blood vessel
19	chr21:44934600-44938200	Enhancers	Right Atrium	heart
20	chr21:44934600-44938400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr21:44934600-44940200	Enhancers	Placenta	Placenta
22	chr21:44935400-44938400	Enhancers	Right Ventricle	heart
23	chr21:44935400-44943400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr21:44935800-44938200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr21:44935800-44938400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:44935800-44938400	Enhancers	Fetal Lung	lung
27	chr21:44936000-44938200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr21:44936000-44938200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr21:44936000-44938400	Enhancers	Psoas Muscle	Psoas
30	chr21:44936200-44938400	Flanking Active TSS	Hela-S3	cervix
31	chr21:44936200-44938600	Flanking Active TSS	NHEK	skin
32	chr21:44936400-44938200	Enhancers	Fetal Kidney	kidney
33	chr21:44936400-44938600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr21:44936600-44938200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr21:44936600-44938200	Enhancers	Fetal Brain Male	brain
36	chr21:44936600-44938400	Enhancers	Colonic Mucosa	Colon
37	chr21:44936600-44938600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr21:44936600-44938600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr21:44936600-44939000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr21:44936800-44938400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr21:44937000-44938200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr21:44937000-44941000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr21:44937200-44938200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr21:44937200-44938400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr21:44937200-44938400	Enhancers	Stomach Mucosa	stomach
46	chr21:44937200-44938400	Weak transcription	Thymus	Thymus
47	chr21:44937200-44938600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr21:44937200-44939000	Enhancers	HSMMtube	muscle
49	chr21:44937200-44941800	Weak transcription	Spleen	Spleen
50	chr21:44937400-44938200	Enhancers	H9 Cell Line	embryonic stem cell

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