Variant report

Variant	rs59114240
Chromosome Location	chr6:31656232-31656233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31654895-31657040	K562	blood:	n/a	n/a
2	POLR2A	chr6:31656005-31656307	K562	blood:	n/a	n/a
3	JUN	chr6:31653818-31659514	K562	blood:	n/a	chr6:31658298-31658308 chr6:31656459-31656468 chr6:31658298-31658308 chr6:31658299-31658307 chr6:31658297-31658309 chr6:31657506-31657518 chr6:31658298-31658308
4	POLR2A	chr6:31654970-31656582	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31656167..31662607-chr6:31701760..31709122,7	MCF-7	breast:
2	chr6:31654755..31657598-chr6:31674069..31676808,2	MCF-7	breast:
3	chr6:31629136..31631208-chr6:31655120..31656869,2	MCF-7	breast:
4	chr6:31650686..31652268-chr6:31655538..31657371,2	MCF-7	breast:
5	chr6:31654964..31657960-chr6:31926410..31928172,2	K562	blood:
6	chr6:31654373..31658459-chr6:31668305..31672590,5	MCF-7	breast:
7	chr6:31647152..31650140-chr6:31654951..31659176,4	MCF-7	breast:
8	chr6:31655444..31658089-chr6:31668201..31670879,2	MCF-7	breast:
9	chr6:31631608..31633822-chr6:31656164..31658364,2	MCF-7	breast:

Variant related genes	Relation type
LY6G5C	TF binding region
ABHD16A	TF binding region
ENSG00000266776	Chromatin interaction
ENSG00000204356	Chromatin interaction
ENSG00000204424	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204410	Chromatin interaction
ENSG00000204428	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000250641	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204351	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000255152	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11961829	0.91[AFR][1000 genomes]
rs11964779	1.00[EUR][1000 genomes]
rs11965323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966331	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11967206	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295666	1.00[ASN][1000 genomes]
rs2295667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399971	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34453162	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713482	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947252	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947329	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947330	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59002496	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60149397	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60559550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60900316	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73398259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398298	0.91[AFR][1000 genomes]
rs7382084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9800604	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31649400-31657000	Weak transcription	Small Intestine	intestine
2	chr6:31649400-31657600	Weak transcription	Psoas Muscle	Psoas
3	chr6:31649400-31658200	Weak transcription	A549	lung
4	chr6:31649600-31657800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:31649600-31658000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:31649600-31669400	Weak transcription	HMEC	breast
7	chr6:31649800-31656600	Weak transcription	GM12878-XiMat	blood
8	chr6:31650800-31668800	Strong transcription	Thymus	Thymus
9	chr6:31651200-31663400	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:31651200-31668600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:31651600-31660000	Weak transcription	Fetal Kidney	kidney
12	chr6:31651600-31664600	Strong transcription	Fetal Thymus	thymus
13	chr6:31651600-31667800	Strong transcription	Brain Germinal Matrix	brain
14	chr6:31651600-31668600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:31651800-31657800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:31651800-31659800	Weak transcription	Fetal Brain Male	brain
17	chr6:31651800-31665400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:31651800-31669200	Weak transcription	Fetal Heart	heart
19	chr6:31652000-31662200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:31652000-31664600	Strong transcription	Placenta	Placenta
21	chr6:31652000-31665600	Strong transcription	Adipose Nuclei	Adipose
22	chr6:31652000-31668000	Strong transcription	Liver	Liver
23	chr6:31652000-31668600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:31652000-31668600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:31652000-31668600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:31652000-31668600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr6:31652000-31668800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:31652200-31656400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr6:31652200-31664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:31652200-31666000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:31652200-31666000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:31652200-31668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:31652200-31668600	Strong transcription	Fetal Stomach	stomach
35	chr6:31652200-31668800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:31652400-31657000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr6:31652400-31657200	Strong transcription	Fetal Intestine Small	intestine
38	chr6:31652400-31657400	Strong transcription	Spleen	Spleen
39	chr6:31652400-31665400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:31652400-31668800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:31652600-31666000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:31653400-31657600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:31653400-31667800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:31653600-31657400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:31653600-31657400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:31653600-31658000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:31653600-31661600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:31653600-31663200	Strong transcription	Brain Angular Gyrus	brain
49	chr6:31653600-31663400	Strong transcription	Right Ventricle	heart
50	chr6:31653600-31664800	Strong transcription	Brain Hippocampus Middle	brain

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