Variant report

Variant	rs4647549
Chromosome Location	chr9:97864686-97864687
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97767984..97771413-chr9:97863181..97865279,3	MCF-7	breast:
2	chr9:97863322..97865050-chr9:97889040..97891690,2	MCF-7	breast:
3	chr9:97677752..97679615-chr9:97863555..97866093,2	MCF-7	breast:
4	chr9:97836720..97838496-chr9:97862659..97865053,2	MCF-7	breast:
5	chr9:97765323..97769705-chr9:97862914..97866422,4	MCF-7	breast:
6	chr9:97863709..97866154-chr9:97872282..97873839,2	MCF-7	breast:
7	chr9:97400366..97403518-chr9:97862496..97865550,3	MCF-7	breast:
8	chr9:97863799..97866898-chr9:97878535..97880902,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000165140	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004813	0.88[GIH][hapmap]
rs10512252	0.88[GIH][hapmap]
rs12683030	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12683182	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs12683564	0.91[ASN][1000 genomes]
rs12683692	0.95[ASN][1000 genomes]
rs12686588	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs16911817	0.88[GIH][hapmap]
rs16911826	0.88[GIH][hapmap]
rs1875835	0.85[JPT][hapmap]
rs2061799	0.86[JPT][hapmap]
rs2078379	0.88[GIH][hapmap]
rs2404458	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs3780566	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs3802449	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3802450	0.91[ASN][1000 genomes]
rs3847309	0.88[GIH][hapmap]
rs4647378	0.85[JPT][hapmap]
rs4647387	0.85[JPT][hapmap]
rs4647397	0.85[JPT][hapmap]
rs4647402	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4647408	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs4647414	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs4647436	0.85[JPT][hapmap]
rs4647437	0.85[JPT][hapmap]
rs4647466	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4647472	0.85[JPT][hapmap]
rs4647473	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4647484	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs4647491	0.85[JPT][hapmap]
rs4647493	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs4647509	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4647510	0.88[CHD][hapmap];1.00[GIH][hapmap]
rs4647514	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs4647516	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs6479596	0.86[JPT][hapmap]
rs6479597	0.86[JPT][hapmap]
rs7022739	0.86[JPT][hapmap]
rs72750391	0.91[ASN][1000 genomes]
rs7854840	0.85[JPT][hapmap]
rs9792415	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs9792533	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking 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 miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
6	chr9:97847600-97878400	Weak transcription	Dnd41	blood
7	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
9	chr9:97855400-97865400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:97855600-97865400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
14	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:97856600-97865200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:97857800-97869600	Weak transcription	HUVEC	blood vessel
17	chr9:97858600-97867600	Genic enhancers	Fetal Muscle Leg	muscle
18	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
19	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:97858800-97870800	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr9:97859000-97865400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:97859600-97865400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:97860000-97875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:97860200-97867000	Enhancers	Fetal Heart	heart
25	chr9:97860400-97867800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:97860400-97879000	Strong transcription	Liver	Liver
27	chr9:97860600-97864800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:97860600-97865000	Enhancers	Esophagus	oesophagus
29	chr9:97860600-97865400	Genic enhancers	Placenta	Placenta
30	chr9:97860600-97869000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:97860600-97870200	Strong transcription	Thymus	Thymus
32	chr9:97861000-97865400	Strong transcription	Fetal Intestine Small	intestine
33	chr9:97861000-97865800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:97861000-97866200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:97861000-97869000	Weak transcription	Fetal Thymus	thymus
36	chr9:97861200-97865000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:97861200-97877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:97861600-97866800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:97861800-97864800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:97861800-97865000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:97862000-97865200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr9:97862000-97865600	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr9:97862200-97864800	Strong transcription	Primary T cells from cord blood	blood
45	chr9:97862200-97865400	Strong transcription	HepG2	liver
46	chr9:97862200-97867200	Enhancers	Brain Substantia Nigra	brain
47	chr9:97862200-97870200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:97862400-97864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:97862400-97864800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:97862400-97865000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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