Variant report

Variant	rs9399297
Chromosome Location	chr6:140193528-140193529
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139695224..139697004-chr6:140192656..140195236,2	K562	blood:
2	chr6:139694303..139697776-chr6:140190370..140193762,4	MCF-7	breast:
3	chr6:140193395..140195194-chr6:140196132..140197957,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs613274	0.84[JPT][hapmap]
rs618471	0.80[JPT][hapmap]
rs6938814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376478	0.80[JPT][hapmap]
rs9385885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389730	0.81[JPT][hapmap]
rs9484321	0.81[JPT][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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140185400-140193800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:140190600-140193600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
4	chr6:140191600-140203000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:140191800-140194800	Enhancers	Fetal Intestine Small	intestine
6	chr6:140192000-140194400	Enhancers	Colon Smooth Muscle	Colon
7	chr6:140192000-140195200	Enhancers	Fetal Intestine Large	intestine
8	chr6:140192400-140194000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:140192400-140194200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:140192600-140194200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:140192600-140194200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:140192600-140194400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:140192800-140193600	Enhancers	Fetal Stomach	stomach
14	chr6:140193000-140194200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:140193200-140193800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:140193200-140194000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:140193200-140194200	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:140193400-140193600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:140193400-140193800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:140193400-140193800	Enhancers	Stomach Smooth Muscle	stomach
21	chr6:140193400-140193800	Enhancers	NHLF	lung
22	chr6:140193400-140194000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:140193400-140194000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:140193400-140194000	Enhancers	Stomach Mucosa	stomach
25	chr6:140193400-140194000	Enhancers	Osteobl	bone
26	chr6:140193400-140194200	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:140193400-140194400	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr6:140193400-140194800	Enhancers	Rectal Mucosa Donor 31	rectum

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