Variant report

Variant	rs31454
Chromosome Location	chr5:16930761-16930762
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16930256..16932203-chr5:16934873..16936431,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10061139	0.92[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650460	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs29448	0.94[MEX][hapmap]
rs29454	0.80[CHD][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs39896	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs31454	SLC35B4	trans	brain	seeQTL
rs31454	MAP3K9	trans	brain	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
2	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
5	chr5:16916000-16930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:16919200-16931600	Weak transcription	HMEC	breast
7	chr5:16920800-16930800	Weak transcription	Fetal Kidney	kidney
8	chr5:16922000-16931400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:16922000-16931600	Weak transcription	Osteobl	bone
10	chr5:16923200-16930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:16923200-16932400	Weak transcription	Gastric	stomach
12	chr5:16924400-16930800	Weak transcription	Lung	lung
13	chr5:16924600-16931600	Weak transcription	Fetal Intestine Small	intestine
14	chr5:16926200-16933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:16928200-16931600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:16929600-16930800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:16929600-16933400	Enhancers	Stomach Mucosa	stomach
18	chr5:16929600-16933600	Enhancers	Pancreas	Pancrea
19	chr5:16929800-16931000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:16929800-16933200	Enhancers	Fetal Lung	lung
21	chr5:16929800-16933800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:16930000-16931200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:16930000-16931200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr5:16930000-16931600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:16930000-16931600	Enhancers	HUVEC	blood vessel
26	chr5:16930200-16931000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:16930200-16931000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:16930200-16931000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:16930200-16931000	Transcr. at gene 5' and 3'	A549	lung
30	chr5:16930200-16931600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:16930200-16931800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr5:16930200-16932600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:16930200-16932800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr5:16930200-16932800	Enhancers	NHDF-Ad	bronchial
35	chr5:16930200-16933400	Enhancers	Ovary	ovary
36	chr5:16930200-16934000	Enhancers	Fetal Intestine Large	intestine
37	chr5:16930200-16934000	Enhancers	Fetal Muscle Leg	muscle
38	chr5:16930400-16931000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:16930400-16931400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:16930400-16931600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr5:16930400-16931600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr5:16930400-16931800	Enhancers	HSMMtube	muscle
43	chr5:16930400-16931800	Genic enhancers	NHEK	skin
44	chr5:16930400-16933000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:16930400-16933000	Enhancers	HSMM	muscle
46	chr5:16930400-16933200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:16930400-16933200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:16930600-16931000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:16930600-16931000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:16930600-16931000	Enhancers	Rectal Mucosa Donor 29	rectum

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