Variant report

Variant	rs836483
Chromosome Location	chr7:6427741-6427742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr7:6427598-6428039	HEK293-T-REx	kidney:	n/a	chr7:6427878-6427887
2	POLR2A	chr7:6427607-6428013	K562	blood:	n/a	n/a
3	POLR2A	chr7:6427583-6428035	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:6427733-6428333	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:6427708-6427960	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6415178..6416975-chr7:6426266..6428182,2	MCF-7	breast:
2	chr7:6421014..6427961-chr7:6430347..6436546,11	K562	blood:
3	chr7:6425039..6427961-chr7:6431283..6434070,6	K562	blood:
4	chr7:6408313..6409948-chr7:6425652..6428069,2	MCF-7	breast:
5	chr7:6423770..6428087-chr7:6429749..6432812,3	MCF-7	breast:

Variant related genes	Relation type
RAC1	TF binding region
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13238780	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2689420	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2742122	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702483	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs702485	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs702486	0.84[CEU][hapmap]
rs73057348	0.86[ASN][1000 genomes]
rs836471	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs836477	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836478	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836480	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836487	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836489	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836492	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs836494	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836499	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836508	0.84[CEU][hapmap]
rs836509	0.84[CEU][hapmap]
rs836513	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs836516	0.85[CEU][hapmap]
rs836526	0.86[ASN][1000 genomes]
rs836527	0.86[ASN][1000 genomes]
rs836529	0.86[ASN][1000 genomes]
rs836534	0.84[CEU][hapmap]
rs836536	0.82[ASN][1000 genomes]
rs836539	0.81[ASN][1000 genomes]
rs836549	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836551	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836556	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836558	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836559	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861369	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs866278	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv605999	chr7:6396719-6472881	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs836483	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6417200-6435400	Weak transcription	Fetal Brain Male	brain
2	chr7:6423000-6432400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:6423800-6427800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr7:6424000-6432400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6424000-6432400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:6424600-6431400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:6425400-6432600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:6425600-6427800	Weak transcription	Colonic Mucosa	Colon
9	chr7:6425600-6432200	Weak transcription	Fetal Heart	heart
10	chr7:6425800-6432600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:6426000-6432400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:6426000-6432400	Weak transcription	Ovary	ovary
13	chr7:6426000-6432400	Weak transcription	Right Atrium	heart
14	chr7:6426000-6456400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:6426200-6430000	Strong transcription	K562	blood
17	chr7:6426200-6431800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:6426400-6431200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:6426400-6432400	Weak transcription	Psoas Muscle	Psoas
20	chr7:6426400-6457400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:6426600-6431800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:6426600-6432000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr7:6426600-6432400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:6426600-6432600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:6426600-6434200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:6426600-6434400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:6426600-6436200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:6426800-6428000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:6426800-6428000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr7:6426800-6428000	Genic enhancers	Hela-S3	cervix
31	chr7:6426800-6428000	Genic enhancers	NHEK	skin
32	chr7:6426800-6428400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:6426800-6428600	Strong transcription	Fetal Kidney	kidney
34	chr7:6426800-6428600	Genic enhancers	A549	lung
35	chr7:6426800-6429200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:6426800-6429600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:6426800-6431400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr7:6426800-6432400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr7:6426800-6432400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr7:6426800-6432400	Strong transcription	GM12878-XiMat	blood
41	chr7:6426800-6432400	Strong transcription	HSMM	muscle
42	chr7:6426800-6432600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:6426800-6434600	Strong transcription	HepG2	liver
44	chr7:6426800-6436200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:6426800-6436400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:6426800-6436600	Strong transcription	Dnd41	blood
47	chr7:6427000-6428000	Genic enhancers	Left Ventricle	heart
48	chr7:6427000-6428400	Strong transcription	Brain Substantia Nigra	brain
49	chr7:6427000-6428800	Strong transcription	HUVEC	blood vessel
50	chr7:6427000-6429000	Strong transcription	NHDF-Ad	bronchial

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