Variant report

Variant	rs6714421
Chromosome Location	chr2:85703308-85703309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
2	chr2:85697443..85708380-chr2:85764609..85769775,19	K562	blood:
3	chr2:85702779..85705594-chr2:85762118..85763957,2	K562	blood:
4	chr2:85702905..85705679-chr2:85766102..85768193,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115486	Chromatin interaction
ENSG00000266577	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10196697	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11126994	0.85[ASN][1000 genomes]
rs11673725	0.82[ASN][1000 genomes]
rs11883636	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12613508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470501	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4993939	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4993940	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7577642	0.92[JPT][hapmap]

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	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6714421	IMMT	cis	cerebellum	SCAN
rs6714421	MAT2A	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85698600-85705600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:85700400-85705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:85700800-85703400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:85700800-85703400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:85702400-85704200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:85702800-85703400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:85702800-85703600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:85702800-85703600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:85702800-85704200	Enhancers	Fetal Intestine Large	intestine
10	chr2:85702800-85704400	Enhancers	Fetal Intestine Small	intestine
11	chr2:85703000-85703400	Enhancers	Colonic Mucosa	Colon
12	chr2:85703000-85703400	Enhancers	Small Intestine	intestine
13	chr2:85703000-85703400	Enhancers	Osteobl	bone
14	chr2:85703000-85703600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:85703000-85703600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:85703000-85703600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:85703000-85703600	Enhancers	Duodenum Mucosa	Duodenum
18	chr2:85703000-85703600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr2:85703000-85703600	Flanking Active TSS	HepG2	liver
20	chr2:85703000-85703600	Enhancers	HSMM	muscle
21	chr2:85703000-85703800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:85703000-85703800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:85703000-85703800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:85703000-85704200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:85703000-85704200	Enhancers	NHEK	skin
26	chr2:85703200-85703400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:85703200-85703400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:85703200-85703400	Enhancers	Esophagus	oesophagus
29	chr2:85703200-85703600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:85703200-85703600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:85703200-85703600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr2:85703200-85703600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:85703200-85703600	Enhancers	Adipose Nuclei	Adipose
34	chr2:85703200-85703600	Flanking Active TSS	Liver	Liver
35	chr2:85703200-85703600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:85703200-85703800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:85703200-85704000	Enhancers	A549	lung
38	chr2:85703200-85704000	Enhancers	HMEC	breast
39	chr2:85703200-85704200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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