Variant report

Variant	rs641027
Chromosome Location	chr13:39979197-39979198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10492739	0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1175912	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1185800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428389	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12429365	0.90[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs1535776	0.93[JPT][hapmap]
rs17803327	0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs516214	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs561008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59279722	0.88[ASN][1000 genomes]
rs629011	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs629422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73173498	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73173499	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576785	0.80[GIH][hapmap]

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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs641027	LHFP	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39960000-39979200	Weak transcription	NHDF-Ad	bronchial
2	chr13:39970200-39979600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:39971200-39980200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:39972400-39979600	Weak transcription	NHLF	lung
5	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
6	chr13:39975800-39979200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr13:39975800-39979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:39975800-39981000	Weak transcription	Right Ventricle	heart
9	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
11	chr13:39976000-39979200	Weak transcription	Fetal Brain Male	brain
12	chr13:39976000-39979400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:39976000-39979600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:39976000-39979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:39976000-39979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr13:39976000-39981000	Weak transcription	Brain Substantia Nigra	brain
17	chr13:39976200-39979200	Weak transcription	Fetal Brain Female	brain
18	chr13:39976200-39979400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:39976200-39979600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:39976200-39979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr13:39976200-39984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:39977000-39979200	Weak transcription	Ovary	ovary
24	chr13:39977000-39980200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:39977200-39981000	Weak transcription	Left Ventricle	heart
27	chr13:39977200-39983800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:39977400-39979400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:39977400-39979600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:39977400-39983600	Weak transcription	Brain Hippocampus Middle	brain
31	chr13:39977600-39979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:39977600-39979400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:39977600-39982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr13:39977800-39984400	Weak transcription	Psoas Muscle	Psoas
35	chr13:39978000-39979400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:39978200-39979400	Weak transcription	Fetal Heart	heart
37	chr13:39979000-39979400	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr13:39979000-39980000	Enhancers	Fetal Lung	lung

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