Variant report

Variant	rs836509
Chromosome Location	chr7:6457655-6457656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6439968..6442839-chr7:6456172..6458248,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13238780	0.96[CEU][hapmap]
rs702483	0.88[CEU][hapmap]
rs702484	0.92[CHB][hapmap]
rs702485	0.88[CEU][hapmap]
rs702486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836472	0.92[CHB][hapmap]
rs836478	0.88[CEU][hapmap]
rs836480	0.88[CEU][hapmap]
rs836483	0.84[CEU][hapmap]
rs836499	0.84[EUR][1000 genomes]
rs836503	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836513	0.84[EUR][1000 genomes]
rs836516	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs836526	0.83[EUR][1000 genomes]
rs836527	0.84[EUR][1000 genomes]
rs836529	0.84[EUR][1000 genomes]
rs836534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836539	0.80[EUR][1000 genomes]
rs836548	0.92[CHB][hapmap]
rs836549	0.84[CEU][hapmap]
rs836551	0.85[CEU][hapmap]
rs836556	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs836558	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs836559	0.96[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv606000	chr7:6446027-6477002	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv887428	chr7:6449496-6463905	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs836509	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6426000-6475600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:6437600-6470400	Strong transcription	Fetal Brain Female	brain
3	chr7:6438000-6458000	Strong transcription	Osteobl	bone
4	chr7:6438000-6462400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:6438600-6475600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:6438800-6462800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:6439400-6458000	Strong transcription	Fetal Muscle Leg	muscle
8	chr7:6439600-6472400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:6439800-6474600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:6439800-6474600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:6439800-6477400	Strong transcription	Fetal Intestine Small	intestine
12	chr7:6440200-6461400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:6440200-6464600	Weak transcription	Right Atrium	heart
14	chr7:6440400-6459400	Strong transcription	Hela-S3	cervix
15	chr7:6440800-6460600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr7:6441200-6471400	Strong transcription	Brain Germinal Matrix	brain
17	chr7:6441400-6458000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:6443800-6465200	Weak transcription	Fetal Heart	heart
19	chr7:6443800-6475000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr7:6444000-6474600	Strong transcription	Lung	lung
21	chr7:6448600-6470000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:6450400-6460600	Weak transcription	Fetal Brain Male	brain
23	chr7:6450400-6475000	Strong transcription	Fetal Stomach	stomach
24	chr7:6452600-6461400	Weak transcription	K562	blood
25	chr7:6452800-6475000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:6453000-6463600	Weak transcription	GM12878-XiMat	blood
27	chr7:6453000-6486800	Weak transcription	Small Intestine	intestine
28	chr7:6453600-6483200	Weak transcription	Fetal Kidney	kidney
29	chr7:6454600-6463600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:6456600-6460200	Weak transcription	HUVEC	blood vessel
31	chr7:6456600-6464400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:6456600-6475200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:6456800-6457800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:6456800-6458600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:6456800-6458800	Weak transcription	Ovary	ovary
36	chr7:6456800-6458800	Weak transcription	HSMMtube	muscle
37	chr7:6456800-6459000	Weak transcription	NHEK	skin
38	chr7:6456800-6460000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:6456800-6460200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:6456800-6460200	Weak transcription	Brain Angular Gyrus	brain
41	chr7:6456800-6460200	Weak transcription	NHDF-Ad	bronchial
42	chr7:6456800-6460400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:6456800-6460400	Weak transcription	Aorta	Aorta
44	chr7:6456800-6461200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:6456800-6461200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:6456800-6464000	Weak transcription	Stomach Mucosa	stomach
47	chr7:6456800-6486800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr7:6457000-6458800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:6457000-6458800	Weak transcription	Pancreas	Pancrea
50	chr7:6457000-6459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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