Variant report

Variant	rs836549
Chromosome Location	chr7:6439945-6439946
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	chr7:6412517..6417079-chr7:6439604..6446019,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10281392	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs12112106	0.82[CHB][hapmap]
rs13238780	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2689420	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs2742122	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4724798	0.82[CHB][hapmap]
rs702483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702485	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs702486	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs73057348	0.90[ASN][1000 genomes]
rs755629	0.81[CHB][hapmap]
rs836477	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836478	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836483	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]
rs836487	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836489	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836492	0.83[AMR][1000 genomes]
rs836494	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836498	0.81[ASN][1000 genomes]
rs836499	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836508	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs836509	0.84[CEU][hapmap]
rs836513	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836516	0.82[CEU][hapmap]
rs836526	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836527	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836529	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836534	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs836536	0.85[ASN][1000 genomes]
rs836539	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs836551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836556	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836558	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836559	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs861369	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs866278	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
8	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
9	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
10	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs836549	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6426000-6456400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:6426400-6457400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6433200-6441200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:6433600-6441200	Weak transcription	Fetal Kidney	kidney
6	chr7:6433800-6440600	Weak transcription	HSMMtube	muscle
7	chr7:6434200-6441200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:6434200-6441200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:6434400-6440800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:6436000-6440200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:6436000-6440800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:6436000-6444800	Weak transcription	Fetal Brain Male	brain
13	chr7:6436200-6440800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:6436200-6441000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:6436200-6441200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:6436200-6448200	Weak transcription	Small Intestine	intestine
17	chr7:6437200-6449000	Strong transcription	Fetal Stomach	stomach
18	chr7:6437400-6440200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:6437400-6440200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:6437400-6440200	Enhancers	Brain Angular Gyrus	brain
21	chr7:6437400-6457400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:6437400-6457400	Strong transcription	Dnd41	blood
23	chr7:6437600-6440200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:6437600-6440200	Enhancers	Fetal Heart	heart
25	chr7:6437600-6440200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr7:6437600-6440200	Enhancers	Stomach Mucosa	stomach
27	chr7:6437600-6440200	Genic enhancers	A549	lung
28	chr7:6437600-6440400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:6437600-6440400	Genic enhancers	HepG2	liver
30	chr7:6437600-6444000	Strong transcription	K562	blood
31	chr7:6437600-6470400	Strong transcription	Fetal Brain Female	brain
32	chr7:6437800-6440200	Genic enhancers	Fetal Thymus	thymus
33	chr7:6437800-6441000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr7:6437800-6441400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:6437800-6441400	Genic enhancers	Lung	lung
36	chr7:6437800-6450200	Strong transcription	Thymus	Thymus
37	chr7:6437800-6456400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:6437800-6457200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:6437800-6457400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr7:6438000-6457400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr7:6438000-6458000	Strong transcription	Osteobl	bone
42	chr7:6438000-6462400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:6438200-6440200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr7:6438200-6440400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:6438200-6445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr7:6438200-6450600	Strong transcription	Colonic Mucosa	Colon
47	chr7:6438400-6440600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr7:6438400-6441200	Weak transcription	Brain Germinal Matrix	brain
49	chr7:6438600-6440800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:6438600-6441200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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