Variant report

Variant	rs11983030
Chromosome Location	chr7:108043641-108043642
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108038876..108042615-chr7:108043454..108045817,3	K562	blood:
2	chr7:108042175..108044661-chr7:108050644..108052443,2	K562	blood:
3	chr7:108040975..108043949-chr7:108092664..108095074,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12333431	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13221639	0.80[GIH][hapmap];0.87[MEX][hapmap]
rs16872525	0.86[CHB][hapmap]
rs1990162	0.92[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2108256	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2158846	0.82[MKK][hapmap]
rs2284290	0.91[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs2284291	0.83[MEX][hapmap]
rs2300037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300043	0.89[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300045	0.83[GIH][hapmap];0.80[MEX][hapmap]
rs2300049	0.81[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2300050	0.82[AFR][1000 genomes]
rs4141076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730307	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730309	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730320	0.80[AFR][1000 genomes]
rs61550883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11983030	LHFPL3	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108024000-108045600	Weak transcription	Brain Anterior Caudate	brain
2	chr7:108035000-108046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:108036400-108049200	Weak transcription	Spleen	Spleen
4	chr7:108036600-108044600	Weak transcription	Brain Substantia Nigra	brain
5	chr7:108036600-108045600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:108036600-108046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:108036600-108048000	Weak transcription	Brain Angular Gyrus	brain
8	chr7:108036600-108048000	Weak transcription	Pancreas	Pancrea
9	chr7:108036600-108054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:108036800-108046600	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:108037000-108044000	Weak transcription	Fetal Brain Male	brain
12	chr7:108037000-108046800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:108039200-108045000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:108040000-108048000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:108040200-108048800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:108040600-108046400	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:108041800-108044400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:108042600-108046600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:108042800-108044200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:108042800-108044800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:108043000-108043800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:108043000-108044200	Enhancers	HMEC	breast
23	chr7:108043000-108044400	Enhancers	HUVEC	blood vessel
24	chr7:108043000-108044600	Enhancers	Fetal Intestine Large	intestine
25	chr7:108043000-108044800	Enhancers	A549	lung
26	chr7:108043200-108043800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr7:108043200-108043800	Enhancers	Brain Cingulate Gyrus	brain
28	chr7:108043400-108043800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:108043400-108044400	Weak transcription	Placenta	Placenta
30	chr7:108043400-108046400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:108043600-108044000	Weak transcription	Fetal Intestine Small	intestine
32	chr7:108043600-108045200	Weak transcription	Fetal Lung	lung
33	chr7:108043600-108046800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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