Variant report

Variant	rs1893602
Chromosome Location	chr9:136659789-136659790
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:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136658078..136660210-chr9:136666155..136667657,2	K562	blood:
2	chr9:136652568..136661500-chr9:136853760..136861284,29	MCF-7	breast:
3	chr9:136652969..136655404-chr9:136657500..136660363,3	K562	blood:
4	chr9:136659151..136663086-chr9:136665860..136670889,7	K562	blood:
5	chr9:136658148..136661518-chr9:136735926..136740986,7	MCF-7	breast:
6	chr9:136656846..136660173-chr9:136849456..136851758,3	MCF-7	breast:
7	chr9:136657372..136661309-chr9:136835277..136837863,3	MCF-7	breast:
8	chr9:136649765..136654574-chr9:136658647..136663860,5	MCF-7	breast:
9	chr9:136657461..136661655-chr9:136857893..136859866,4	K562	blood:
10	chr9:136655858..136660240-chr9:136726638..136729094,3	MCF-7	breast:
11	chr9:136657048..136659894-chr9:136660095..136663182,3	MCF-7	breast:
12	chr9:136658683..136660342-chr9:136699165..136701047,2	MCF-7	breast:
13	chr9:136655680..136661750-chr9:136735179..136740692,8	MCF-7	breast:
14	chr9:136657846..136660757-chr9:136705062..136707156,2	MCF-7	breast:
15	chr9:136658394..136660718-chr9:136671881..136674507,3	MCF-7	breast:
16	chr9:136645262..136664386-chr9:136851810..136861142,57	MCF-7	breast:
17	chr9:136656812..136664739-chr9:136743672..136748217,7	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DBH-6	chr9:136659497-136660036	NONHSAT135344

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10119331	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10121278	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761399	0.84[EUR][1000 genomes]
rs10993802	0.92[EUR][1000 genomes]
rs10993803	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073888	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073889	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073890	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073891	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073892	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239912	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239913	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2428099	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488561	0.80[EUR][1000 genomes]
rs3824560	0.94[EUR][1000 genomes]
rs3824561	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479623	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7019167	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025087	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032391	0.84[EUR][1000 genomes]
rs7032952	0.85[EUR][1000 genomes]
rs7038080	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038187	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039067	0.84[EUR][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	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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
rs1893602	AL590710.1	cis	Esophagus Muscularis	GTEx
rs1893602	VAV2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136640000-136679400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:136640400-136682600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:136640800-136667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:136643200-136689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:136643800-136672600	Weak transcription	Aorta	Aorta
6	chr9:136645000-136664200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:136650000-136679400	Weak transcription	Right Atrium	heart
8	chr9:136650600-136688800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:136651400-136668200	Weak transcription	NH-A	brain
10	chr9:136651400-136686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:136651400-136689000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:136654000-136668200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:136654000-136671000	Weak transcription	Esophagus	oesophagus
14	chr9:136654000-136683600	Weak transcription	Small Intestine	intestine
15	chr9:136655200-136659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:136655200-136665400	Strong transcription	NHEK	skin
17	chr9:136655200-136669600	Weak transcription	Right Ventricle	heart
18	chr9:136656000-136664000	Weak transcription	Thymus	Thymus
19	chr9:136656400-136659800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:136656400-136661000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:136656600-136671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:136657000-136672400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:136657200-136660800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:136657200-136672600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:136657600-136661000	Enhancers	Primary B cells from cord blood	blood
26	chr9:136657600-136668600	Weak transcription	NHDF-Ad	bronchial
27	chr9:136657600-136672200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:136657800-136671800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:136657800-136690600	Weak transcription	Fetal Kidney	kidney
30	chr9:136658000-136660000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:136658000-136660200	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr9:136658000-136660200	Enhancers	Fetal Thymus	thymus
33	chr9:136658200-136660200	Genic enhancers	GM12878-XiMat	blood
34	chr9:136658600-136661200	Strong transcription	Hela-S3	cervix
35	chr9:136658600-136669800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:136658600-136670400	Weak transcription	Brain Substantia Nigra	brain
37	chr9:136658600-136680800	Strong transcription	Fetal Intestine Large	intestine
38	chr9:136658600-136691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:136658800-136659800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:136658800-136659800	Weak transcription	HSMM	muscle
41	chr9:136658800-136659800	Weak transcription	Osteobl	bone
42	chr9:136658800-136660000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:136658800-136660000	Genic enhancers	Fetal Muscle Leg	muscle
44	chr9:136658800-136660400	Weak transcription	Fetal Lung	lung
45	chr9:136658800-136663400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:136658800-136664600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:136658800-136668200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:136658800-136668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:136658800-136668200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:136658800-136668600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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