Variant report

Variant	rs3824560
Chromosome Location	chr9:136657869-136657870
allele	C/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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136652568..136661500-chr9:136853760..136861284,29	MCF-7	breast:
2	chr9:136652969..136655404-chr9:136657500..136660363,3	K562	blood:
3	chr9:136642803..136649542-chr9:136652545..136658247,6	MCF-7	breast:
4	chr9:136657819..136658763-chr9:136858806..136859951,5	MCF-7	breast:
5	chr9:136657049..136659190-chr9:136665204..136667525,2	MCF-7	breast:
6	chr9:136657265..136659232-chr9:136854243..136855846,2	K562	blood:
7	chr9:136656846..136660173-chr9:136849456..136851758,3	MCF-7	breast:
8	chr9:136657372..136661309-chr9:136835277..136837863,3	MCF-7	breast:
9	chr9:136657809..136658776-chr9:136707143..136707993,3	MCF-7	breast:
10	chr9:136657461..136661655-chr9:136857893..136859866,4	K562	blood:
11	chr9:136655858..136660240-chr9:136726638..136729094,3	MCF-7	breast:
12	chr9:136657048..136659894-chr9:136660095..136663182,3	MCF-7	breast:
13	chr9:136657835..136658758-chr9:136963973..136964578,4	K562	blood:
14	chr9:136655680..136661750-chr9:136735179..136740692,8	MCF-7	breast:
15	chr9:136657846..136660757-chr9:136705062..136707156,2	MCF-7	breast:
16	chr6:28758828..28759555-chr9:136657868..136658790,2	MCF-7	breast:
17	chr9:136645262..136664386-chr9:136851810..136861142,57	MCF-7	breast:
18	chr9:136656812..136664739-chr9:136743672..136748217,7	MCF-7	breast:
19	chr9:136657511..136659120-chr9:136859180..136860603,16	MCF-7	breast:
20	chr9:136657412..136658751-chr9:136858523..136860164,12	K562	blood:
21	chr9:136657344..136658870-chr9:136843564..136845093,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10119331	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121278	0.95[EUR][1000 genomes]
rs10761399	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821524	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10821525	0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10993802	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993803	0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13283160	0.83[ASN][1000 genomes]
rs13292058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1468127	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1893602	0.94[EUR][1000 genomes]
rs2023664	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2023665	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2073888	0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2073889	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2073890	0.92[EUR][1000 genomes]
rs2073891	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2073892	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2073910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2106373	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2239912	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2239913	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2258889	0.91[ASN][1000 genomes]
rs2261613	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2428099	0.81[CHB][hapmap];0.94[EUR][1000 genomes]
rs2488561	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2510239	0.90[ASN][1000 genomes]
rs3824558	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479623	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7019167	0.94[EUR][1000 genomes]
rs7025087	0.94[EUR][1000 genomes]
rs7027503	0.92[ASN][1000 genomes]
rs7032391	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7032952	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7038080	0.81[CHB][hapmap];0.94[EUR][1000 genomes]
rs7038187	0.94[EUR][1000 genomes]
rs7039067	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv466622	chr9:136617292-136658816	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv615691	chr9:136617292-136658816	Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv894118	chr9:136624542-136678954	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv894119	chr9:136629399-136657960	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv894120	chr9:136629399-136662638	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv894121	chr9:136629399-136692787	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3824560	VAV2	cis	Esophagus Muscularis	GTEx
rs3824560	AL590710.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136640000-136658000	Weak transcription	Fetal Thymus	thymus
2	chr9:136640000-136679400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:136640200-136658000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:136640200-136659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:136640400-136682600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:136640800-136667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:136643000-136658000	Weak transcription	Left Ventricle	heart
8	chr9:136643200-136689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:136643800-136672600	Weak transcription	Aorta	Aorta
10	chr9:136644800-136658000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:136645000-136664200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:136645200-136658000	Strong transcription	Fetal Stomach	stomach
13	chr9:136646600-136658000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:136648600-136658200	Weak transcription	Fetal Heart	heart
15	chr9:136650000-136679400	Weak transcription	Right Atrium	heart
16	chr9:136650600-136688800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:136651400-136668200	Weak transcription	NH-A	brain
18	chr9:136651400-136686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:136651400-136689000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:136651600-136658000	Weak transcription	A549	lung
21	chr9:136651600-136658000	Weak transcription	HMEC	breast
22	chr9:136651600-136658400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:136651600-136658400	Weak transcription	Ovary	ovary
24	chr9:136652600-136658000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:136653000-136658600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:136654000-136658400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:136654000-136668200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:136654000-136671000	Weak transcription	Esophagus	oesophagus
29	chr9:136654000-136683600	Weak transcription	Small Intestine	intestine
30	chr9:136654400-136658400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:136654800-136658000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:136654800-136658400	Weak transcription	Fetal Brain Male	brain
33	chr9:136655200-136658000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:136655200-136658000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:136655200-136658000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:136655200-136659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:136655200-136665400	Strong transcription	NHEK	skin
38	chr9:136655200-136669600	Weak transcription	Right Ventricle	heart
39	chr9:136655400-136658000	Weak transcription	Adipose Nuclei	Adipose
40	chr9:136655400-136658000	Weak transcription	Brain Angular Gyrus	brain
41	chr9:136655400-136658000	Weak transcription	Brain Anterior Caudate	brain
42	chr9:136655400-136658000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr9:136655400-136658000	Weak transcription	Brain Hippocampus Middle	brain
44	chr9:136655400-136658000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:136655400-136658000	Weak transcription	Brain Substantia Nigra	brain
46	chr9:136655400-136658000	Weak transcription	HUVEC	blood vessel
47	chr9:136655400-136658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:136655400-136658800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:136655800-136658000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:136656000-136658400	Weak transcription	Colonic Mucosa	Colon

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