Variant report

Variant	rs836489
Chromosome Location	chr7:6418673-6418674
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6412400..6417963-chr7:6418207..6425853,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136238	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2689420	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2742122	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs702483	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702485	0.84[AMR][1000 genomes]
rs836477	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836478	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836480	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836483	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836487	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836492	0.88[AMR][1000 genomes]
rs836494	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836499	0.82[ASN][1000 genomes]
rs836549	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836551	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs836556	0.82[ASN][1000 genomes]
rs836558	0.82[ASN][1000 genomes]
rs836559	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs861369	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs866278	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	nsv967451	chr7:6417630-6427589	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs836489	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	chr7:6415600-6423800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:6415800-6418800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:6415800-6419400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:6415800-6419400	Weak transcription	Aorta	Aorta
5	chr7:6415800-6419600	Weak transcription	HSMMtube	muscle
6	chr7:6415800-6422400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:6415800-6422600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:6415800-6427400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:6416000-6419600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:6416000-6424800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:6416200-6418800	Enhancers	Primary B cells from cord blood	blood
12	chr7:6416200-6421200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:6416200-6422600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:6416400-6420600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:6416400-6422400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:6416600-6423800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:6416800-6418800	Genic enhancers	Fetal Intestine Small	intestine
18	chr7:6416800-6419200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:6416800-6419400	Weak transcription	NH-A	brain
20	chr7:6416800-6419600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:6417000-6419600	Weak transcription	HMEC	breast
22	chr7:6417000-6419600	Weak transcription	NHLF	lung
23	chr7:6417000-6421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:6417000-6422400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:6417000-6427400	Weak transcription	Thymus	Thymus
26	chr7:6417200-6419000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:6417200-6419600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:6417200-6419600	Weak transcription	HSMM	muscle
29	chr7:6417200-6419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:6417200-6419800	Enhancers	Ovary	ovary
31	chr7:6417200-6421400	Enhancers	Psoas Muscle	Psoas
32	chr7:6417200-6422600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:6417200-6426400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:6417200-6435400	Weak transcription	Fetal Brain Male	brain
35	chr7:6417400-6419400	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr7:6417400-6421600	Weak transcription	Esophagus	oesophagus
37	chr7:6417600-6418800	Enhancers	Liver	Liver
38	chr7:6417600-6419200	Strong transcription	Osteobl	bone
39	chr7:6417600-6419400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:6417600-6419600	Weak transcription	Fetal Kidney	kidney
41	chr7:6417600-6422400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:6417600-6423000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:6417800-6418800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:6417800-6418800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:6417800-6418800	Weak transcription	Colonic Mucosa	Colon
46	chr7:6417800-6418800	Enhancers	Duodenum Mucosa	Duodenum
47	chr7:6417800-6418800	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:6417800-6418800	Weak transcription	NHEK	skin
49	chr7:6417800-6419000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:6417800-6419000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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