Variant report

Variant	rs10948782
Chromosome Location	chr6:53702275-53702276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53657031..53659924-chr6:53702076..53704577,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10456673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs10456674	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10948785	0.87[AMR][1000 genomes]
rs11962552	0.87[CHD][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs11970064	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192689	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12200971	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201245	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12201913	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12202128	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12202762	1.00[CHB][hapmap]
rs12204130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12206209	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211130	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211680	0.86[JPT][hapmap]
rs12213392	0.86[JPT][hapmap]
rs12213577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12214863	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211528	1.00[JPT][hapmap]
rs17748374	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35971619	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3935663	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4389767	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678884	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55931905	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919015	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7739668	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745930	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7762326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10948782	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
4	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
5	chr6:53694000-53708400	Weak transcription	Fetal Thymus	thymus
6	chr6:53695000-53702600	Weak transcription	Gastric	stomach
7	chr6:53695000-53705600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:53696200-53702600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:53696400-53708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:53696600-53702600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:53698000-53702600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:53698200-53702600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:53698200-53702800	Weak transcription	HSMMtube	muscle
19	chr6:53698200-53702800	Weak transcription	HUVEC	blood vessel
20	chr6:53698400-53702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:53698600-53702600	Weak transcription	HMEC	breast
22	chr6:53699000-53704800	Weak transcription	Fetal Intestine Small	intestine
23	chr6:53699200-53702600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:53699200-53703400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:53699400-53702400	Weak transcription	Fetal Heart	heart
26	chr6:53699400-53702600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:53699400-53702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:53699400-53709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:53700000-53704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:53700200-53703000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:53700400-53709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:53700800-53702400	Enhancers	Brain Germinal Matrix	brain
33	chr6:53701000-53702800	Weak transcription	HepG2	liver
34	chr6:53701200-53702600	Weak transcription	Pancreas	Pancrea
35	chr6:53701400-53702600	Enhancers	Rectal Smooth Muscle	rectum
36	chr6:53701600-53702800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:53701800-53702400	Enhancers	Brain Hippocampus Middle	brain
38	chr6:53701800-53702600	Enhancers	Brain Angular Gyrus	brain
39	chr6:53701800-53702600	Weak transcription	Brain Substantia Nigra	brain
40	chr6:53702000-53702600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:53702000-53702600	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr6:53702000-53702800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:53702000-53702800	Enhancers	Brain Cingulate Gyrus	brain
44	chr6:53702000-53703200	Enhancers	NHEK	skin
45	chr6:53702000-53704600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:53702200-53702400	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr6:53702200-53703000	Enhancers	Thymus	Thymus
48	chr6:53702200-53703600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr6:53702200-53704400	Enhancers	Colon Smooth Muscle	Colon

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