Variant report

Variant	rs237004
Chromosome Location	chr6:149750334-149750335
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149380842..149383187-chr6:149749461..149751628,2	MCF-7	breast:
2	chr6:149745176..149748304-chr6:149748732..149751749,4	MCF-7	breast:
3	chr6:149749225..149751406-chr6:149752259..149754784,2	K562	blood:
4	chr6:149381576..149384224-chr6:149749932..149753109,3	MCF-7	breast:
5	chr6:149748841..149750725-chr6:149751621..149753759,2	K562	blood:
6	chr6:149749032..149751401-chr6:149754918..149757804,2	K562	blood:
7	chr6:149398184..149404330-chr6:149748783..149757211,17	MCF-7	breast:
8	chr6:149638278..149640828-chr6:149750311..149753449,4	MCF-7	breast:
9	chr6:149352319..149353862-chr6:149749427..149751302,2	MCF-7	breast:
10	chr6:149744819..149747181-chr6:149748180..149751163,2	MCF-7	breast:
11	chr6:149394698..149396657-chr6:149749436..149751094,2	MCF-7	breast:
12	chr6:149748430..149751387-chr6:149751741..149754089,3	MCF-7	breast:
13	chr6:149742080..149743974-chr6:149748766..149751309,2	MCF-7	breast:
14	chr6:149638351..149641682-chr6:149748296..149751639,3	MCF-7	breast:
15	chr6:149407753..149410844-chr6:149747576..149751159,3	MCF-7	breast:
16	chr6:149351119..149355583-chr6:149748923..149756337,13	MCF-7	breast:
17	chr6:149703892..149707802-chr6:149748749..149751962,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11155656	0.82[ASN][1000 genomes]
rs11155657	0.83[ASN][1000 genomes]
rs112225	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs12110948	0.85[ASN][1000 genomes]
rs12190660	0.82[ASN][1000 genomes]
rs173140	0.85[ASN][1000 genomes]
rs1737336	0.82[ASN][1000 genomes]
rs1737337	0.83[ASN][1000 genomes]
rs1749227	0.82[ASN][1000 genomes]
rs1999970	0.84[ASN][1000 genomes]
rs2095849	0.83[ASN][1000 genomes]
rs236997	0.85[ASN][1000 genomes]
rs236998	0.85[ASN][1000 genomes]
rs236999	0.85[ASN][1000 genomes]
rs237000	0.85[ASN][1000 genomes]
rs237013	0.82[ASN][1000 genomes]
rs237014	0.86[ASN][1000 genomes]
rs237015	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs237017	0.86[ASN][1000 genomes]
rs237027	0.91[JPT][hapmap]
rs237032	0.91[JPT][hapmap]
rs237033	0.91[JPT][hapmap]
rs367161	0.84[ASN][1000 genomes]
rs367812	0.84[ASN][1000 genomes]
rs370471	0.84[ASN][1000 genomes]
rs372994	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs373596	0.83[ASN][1000 genomes]
rs374616	0.83[ASN][1000 genomes]
rs376269	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs376757	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs377454	0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs377532	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs378991	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs381226	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs381793	0.84[ASN][1000 genomes]
rs382084	0.84[ASN][1000 genomes]
rs382720	0.93[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs383092	0.84[ASN][1000 genomes]
rs384163	0.84[ASN][1000 genomes]
rs384306	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs384913	0.84[ASN][1000 genomes]
rs385303	0.84[ASN][1000 genomes]
rs388335	0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs393713	0.84[ASN][1000 genomes]
rs394375	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs395037	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs398159	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs403419	0.84[ASN][1000 genomes]
rs405486	0.83[ASN][1000 genomes]
rs407260	0.84[ASN][1000 genomes]
rs408451	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs409196	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs410579	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs411091	0.93[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs411308	0.84[ASN][1000 genomes]
rs416044	0.82[ASN][1000 genomes]
rs419562	0.82[ASN][1000 genomes]
rs419997	0.84[ASN][1000 genomes]
rs425278	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs431362	0.87[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs431978	0.93[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs432582	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs436645	0.83[ASN][1000 genomes]
rs437931	0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs439369	0.84[ASN][1000 genomes]
rs439495	0.93[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs440613	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs450344	0.84[ASN][1000 genomes]
rs452586	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs474726	0.91[JPT][hapmap]
rs480670	0.91[JPT][hapmap]
rs483877	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs484969	0.91[JPT][hapmap]
rs499270	0.84[ASN][1000 genomes]
rs500860	0.91[JPT][hapmap]
rs505765	0.89[JPT][hapmap]
rs506573	0.91[JPT][hapmap]
rs506779	0.91[JPT][hapmap]
rs538706	0.91[JPT][hapmap]
rs543489	0.84[ASN][1000 genomes]
rs548083	0.89[JPT][hapmap]
rs558044	0.91[JPT][hapmap]
rs567816	0.91[JPT][hapmap]
rs569730	0.91[JPT][hapmap]
rs580499	0.91[JPT][hapmap]
rs602010	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs602094	0.84[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7742990	0.91[JPT][hapmap]
rs786749	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs786750	0.80[ASN][1000 genomes]
rs786751	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs814181	0.84[ASN][1000 genomes]
rs9485396	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv517606	chr6:149744632-149755695	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs237004	LRP11	cis	cerebellum	SCAN
rs237004	LRP11	cis	parietal	SCAN
rs237004	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149745400-149750400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:149745600-149752800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:149745600-149752800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:149745600-149752800	Weak transcription	HSMM	muscle
5	chr6:149745600-149753000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:149745600-149753000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:149745600-149753000	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:149746800-149753000	Weak transcription	Placenta	Placenta
9	chr6:149746800-149762000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:149748800-149753200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:149749400-149753400	Weak transcription	HSMMtube	muscle
12	chr6:149749800-149764400	Weak transcription	Right Atrium	heart
13	chr6:149750200-149750600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:149750200-149750800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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