Variant report

Variant	rs11938345
Chromosome Location	chr4:87812621-87812622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87515391..87517685-chr4:87812251..87815383,4	MCF-7	breast:
2	chr4:87514124..87517809-chr4:87811943..87814768,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-2	chr4:87812609-87812746	NONHSAT097286

Variant related genes	Relation type
ENSG00000109339	Chromatin interaction
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11937088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012122	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823793	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7687489	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87806800-87813000	Weak transcription	Left Ventricle	heart
2	chr4:87807200-87812800	Weak transcription	Brain Anterior Caudate	brain
3	chr4:87811800-87812800	Flanking Active TSS	Fetal Lung	lung
4	chr4:87811800-87813000	Flanking Active TSS	NHEK	skin
5	chr4:87812000-87812800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:87812000-87812800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:87812000-87812800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:87812000-87812800	Enhancers	Brain Germinal Matrix	brain
9	chr4:87812000-87812800	Enhancers	Brain Substantia Nigra	brain
10	chr4:87812000-87812800	Enhancers	Placenta	Placenta
11	chr4:87812000-87812800	Enhancers	HUVEC	blood vessel
12	chr4:87812000-87813800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr4:87812000-87814400	Active TSS	Esophagus	oesophagus
14	chr4:87812200-87812800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:87812200-87812800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:87812200-87813000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:87812200-87813000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:87812200-87814000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr4:87812400-87812800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:87812400-87812800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr4:87812400-87812800	Enhancers	NHDF-Ad	bronchial
22	chr4:87812400-87813000	ZNF genes & repeats	Fetal Brain Male	brain
23	chr4:87812400-87813400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:87812400-87813800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:87812400-87813800	Active TSS	Hela-S3	cervix
26	chr4:87812400-87814000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:87812600-87812800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:87812600-87812800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:87812600-87812800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:87812600-87812800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr4:87812600-87812800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr4:87812600-87812800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:87812600-87812800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:87812600-87812800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:87812600-87812800	Enhancers	Primary B cells from peripheral blood	blood
36	chr4:87812600-87812800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr4:87812600-87812800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr4:87812600-87812800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr4:87812600-87812800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
40	chr4:87812600-87812800	Enhancers	Liver	Liver
41	chr4:87812600-87812800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr4:87812600-87812800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr4:87812600-87812800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:87812600-87812800	Active TSS	Fetal Brain Female	brain
45	chr4:87812600-87812800	Enhancers	Fetal Intestine Small	intestine
46	chr4:87812600-87812800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr4:87812600-87812800	Enhancers	HepG2	liver
48	chr4:87812600-87812800	Enhancers	NH-A	brain
49	chr4:87812600-87812800	Active TSS	Osteobl	bone
50	chr4:87812600-87813000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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