Variant report

Variant	rs4627854
Chromosome Location	chr4:85872414-85872415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85871995..85875052-chr4:85885943..85888093,3	MCF-7	breast:
2	chr4:85871120..85875052-chr4:85876385..85879344,3	MCF-7	breast:
3	chr4:85857756..85860501-chr4:85872176..85873960,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180769	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17369165	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs72664967	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4627854	LIN54	cis	parietal	SCAN
rs4627854	AGPAT4	trans	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:85809000-85872800	Weak transcription	A549	lung
3	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:85849200-85876000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85851200-85876000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:85860600-85872800	Weak transcription	Esophagus	oesophagus
7	chr4:85860600-85877000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:85860800-85872800	Weak transcription	NH-A	brain
9	chr4:85861200-85873600	Weak transcription	HUVEC	blood vessel
10	chr4:85863400-85872600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:85864200-85872800	Weak transcription	HSMM	muscle
12	chr4:85864400-85873200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:85864400-85876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:85864400-85877200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:85865200-85876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
19	chr4:85866400-85872800	Weak transcription	Pancreas	Pancrea
20	chr4:85866400-85873200	Weak transcription	NHLF	lung
21	chr4:85866400-85879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:85866600-85873200	Weak transcription	Osteobl	bone
23	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:85867800-85878600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:85869600-85872600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:85869600-85879800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:85869800-85872600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:85869800-85872800	Weak transcription	HSMMtube	muscle
29	chr4:85869800-85873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:85869800-85873200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:85869800-85879200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:85870000-85872800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:85870000-85872800	Weak transcription	NHDF-Ad	bronchial
34	chr4:85870000-85876000	Weak transcription	Left Ventricle	heart
35	chr4:85870200-85872600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:85870200-85872800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:85870200-85872800	Weak transcription	Brain Substantia Nigra	brain
38	chr4:85870200-85872800	Weak transcription	Psoas Muscle	Psoas
39	chr4:85870200-85873000	Weak transcription	Right Ventricle	heart
40	chr4:85870200-85876000	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:85870200-85879200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:85870400-85872800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:85870400-85872800	Weak transcription	Brain Angular Gyrus	brain
44	chr4:85870400-85872800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:85870400-85872800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:85870400-85876000	Weak transcription	Fetal Kidney	kidney
47	chr4:85870400-85876000	Weak transcription	Ovary	ovary
48	chr4:85870400-85876000	Weak transcription	Right Atrium	heart
49	chr4:85870400-85879200	Weak transcription	Adipose Nuclei	Adipose
50	chr4:85870400-85880800	Weak transcription	Primary monocytes fromperipheralblood	blood

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