Variant report

Variant	rs17674953
Chromosome Location	chr5:127278489-127278490
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	chr5:127277558..127280504-chr5:127284897..127288204,4	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10040931	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10519966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745023	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17164449	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839662	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860058	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041143	1.00[JPT][hapmap]
rs35454950	0.82[ASW][hapmap];0.85[CEU][hapmap];0.82[YRI][hapmap]
rs3749746	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56053416	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56100852	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181801	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275766	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59913942	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895467	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897057	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792230	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72792241	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792242	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792259	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711592	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713304	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719691	0.86[CEU][hapmap]
rs7722601	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17674953	HINT1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127267400-127292200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:127269800-127292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:127274400-127287000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
7	chr5:127276600-127278600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:127276600-127279200	Enhancers	Small Intestine	intestine
9	chr5:127276600-127281800	Enhancers	A549	lung
10	chr5:127276800-127278600	Enhancers	Fetal Intestine Small	intestine
11	chr5:127276800-127278600	Enhancers	NHDF-Ad	bronchial
12	chr5:127276800-127278600	Enhancers	NHLF	lung
13	chr5:127277000-127278600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr5:127277000-127279400	Enhancers	Stomach Mucosa	stomach
15	chr5:127277200-127280000	Enhancers	HUVEC	blood vessel
16	chr5:127277400-127278600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr5:127277600-127278600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:127277600-127279400	Weak transcription	Gastric	stomach
19	chr5:127277800-127278600	Enhancers	NHEK	skin
20	chr5:127277800-127278800	Enhancers	GM12878-XiMat	blood
21	chr5:127277800-127278800	Enhancers	Hela-S3	cervix
22	chr5:127278000-127278600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:127278000-127278600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:127278000-127278600	Enhancers	Osteobl	bone
25	chr5:127278000-127278800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:127278000-127279800	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:127278200-127278600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:127278200-127278600	Enhancers	Brain Angular Gyrus	brain
29	chr5:127278200-127279200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:127278400-127278600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:127278400-127279000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:127278400-127281800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:127278400-127283000	Weak transcription	HMEC	breast
34	chr5:127278400-127286400	Weak transcription	Fetal Intestine Large	intestine
35	chr5:127278400-127286400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:127278400-127292800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:127278400-127292800	Weak transcription	Brain Substantia Nigra	brain
38	chr5:127278400-127292800	Weak transcription	HSMM	muscle
39	chr5:127278400-127294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle

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