Variant report

Variant	rs12202128
Chromosome Location	chr6:53733210-53733211
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53725023..53728197-chr6:53731513..53733872,3	K562	blood:
2	chr6:53657682..53662159-chr6:53731929..53736372,8	MCF-7	breast:
3	chr6:53659174..53661919-chr6:53730031..53734887,4	MCF-7	breast:
4	chr6:53731424..53733383-chr6:53740788..53743040,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10948782	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10948785	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11970064	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192118	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192689	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12195491	0.92[EUR][1000 genomes]
rs12200971	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12201245	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12201913	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202361	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12206209	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211130	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12214863	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17748374	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35971619	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3935663	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389767	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4639324	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55678884	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55931905	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6919015	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7739668	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7745930	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7762326	0.91[AMR][1000 genomes];0.91[EUR][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
rs12202128	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:53720600-53741400	Weak transcription	Dnd41	blood
5	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
6	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
8	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
9	chr6:53728200-53734200	Weak transcription	HUVEC	blood vessel
10	chr6:53728400-53734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:53728600-53738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:53728600-53738600	Weak transcription	NHEK	skin
13	chr6:53729000-53733600	Weak transcription	Fetal Stomach	stomach
14	chr6:53729000-53734800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:53729000-53734800	Weak transcription	HMEC	breast
16	chr6:53729400-53736600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:53729400-53738800	Weak transcription	Pancreas	Pancrea
18	chr6:53729400-53748000	Weak transcription	HepG2	liver
19	chr6:53729600-53734400	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:53729800-53734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:53730000-53734800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
24	chr6:53730400-53737200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:53730400-53743800	Weak transcription	Fetal Heart	heart
26	chr6:53731400-53734800	Weak transcription	Brain Substantia Nigra	brain
27	chr6:53732000-53733800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:53732000-53739400	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
30	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
31	chr6:53732400-53734000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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