Variant report

Variant	rs12344461
Chromosome Location	chr9:136919400-136919401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136904281..136909955-chr9:136916883..136922324,6	MCF-7	breast:
2	chr9:136891192..136895857-chr9:136919376..136921931,6	MCF-7	breast:
3	chr9:136913228..136917389-chr9:136917645..136921079,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR5-1	chr9:136919392-136920570	NONHSAT135371

Variant related genes	Relation type
ENSG00000169925	Chromatin interaction
ENSG00000235106	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10993903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342584	0.99[AFR][1000 genomes]
rs12342654	0.96[AFR][1000 genomes]
rs12345376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12345465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12345566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12346699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12353471	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28582206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28694795	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73558800	1.00[EUR][1000 genomes]
rs7854376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv428226	chr9:136825035-136994606	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv894135	chr9:136839840-136927657	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv894136	chr9:136839840-136938961	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv894137	chr9:136839840-136950691	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv894139	chr9:136863932-136950691	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv894140	chr9:136865879-136927657	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
12	nsv894141	chr9:136865879-136938961	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv466627	chr9:136870787-136938961	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv615774	chr9:136870787-136938961	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
16	nsv894145	chr9:136874066-136925451	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv894146	chr9:136874066-136938961	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv894147	chr9:136874066-136950691	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
19	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
20	nsv894149	chr9:136874158-136950691	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
21	nsv894150	chr9:136887757-136944827	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
22	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
23	nsv466629	chr9:136893867-136938961	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
24	nsv615779	chr9:136893867-136938961	Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
25	esv1806029	chr9:136906752-136933825	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv430110	chr9:136909280-136964450	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136891800-136919400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:136892000-136919400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:136892000-136919600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:136892000-136920200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:136892000-136921200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:136892000-136922800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:136892400-136920400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:136892600-136919400	Strong transcription	Fetal Thymus	thymus
9	chr9:136893800-136920000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:136894400-136920200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:136895800-136920000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:136895800-136920000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:136896200-136920600	Strong transcription	Dnd41	blood
14	chr9:136899200-136924600	Weak transcription	GM12878-XiMat	blood
15	chr9:136901600-136923600	Weak transcription	HUVEC	blood vessel
16	chr9:136903000-136919400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:136903000-136919600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:136903600-136919600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr9:136903600-136920000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:136903600-136927000	Strong transcription	Thymus	Thymus
21	chr9:136903800-136919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:136904200-136919800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:136904400-136919800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:136904600-136920800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:136904800-136920600	Strong transcription	Fetal Brain Female	brain
26	chr9:136904800-136920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:136905200-136919800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:136905200-136919800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:136905200-136920400	Weak transcription	Small Intestine	intestine
30	chr9:136906600-136920600	Strong transcription	Fetal Stomach	stomach
31	chr9:136906800-136920400	Strong transcription	Brain Germinal Matrix	brain
32	chr9:136907000-136920000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:136907200-136920000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:136907600-136920400	Weak transcription	Fetal Heart	heart
35	chr9:136909400-136919800	Strong transcription	HepG2	liver
36	chr9:136909800-136919600	Strong transcription	NHLF	lung
37	chr9:136910200-136920400	Weak transcription	Fetal Brain Male	brain
38	chr9:136910200-136920600	Weak transcription	NH-A	brain
39	chr9:136910600-136921000	Weak transcription	Fetal Kidney	kidney
40	chr9:136913200-136920000	Weak transcription	HMEC	breast
41	chr9:136913800-136921000	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr9:136914600-136924200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:136914800-136919400	Strong transcription	Esophagus	oesophagus
44	chr9:136914800-136923800	Weak transcription	Primary B cells from cord blood	blood
45	chr9:136915000-136919400	Weak transcription	Right Atrium	heart
46	chr9:136915400-136920200	Weak transcription	Stomach Mucosa	stomach
47	chr9:136915600-136925000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:136916400-136920600	Weak transcription	A549	lung
49	chr9:136916600-136919600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr9:136916600-136920600	Weak transcription	HSMMtube	muscle

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