Variant report

Variant	rs59002496
Chromosome Location	chr6:31693099-31693100
allele	A/C
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	chr6:31692462-31693144	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr6:31691040-31693231	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:6977978..6980643-chr6:31692087..31694537,2	K562	blood:
2	chr6:31690682..31694598-chr6:31702821..31705560,3	MCF-7	breast:
3	chr6:31691508..31694089-chr6:31833042..31835774,2	K562	blood:

Variant related genes	Relation type
LY6G6C	TF binding region
ENSG00000213719	Chromatin interaction
ENSG00000111669	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11964779	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11965323	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11966331	1.00[EUR][1000 genomes]
rs11967206	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2254083	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2295666	0.83[ASN][1000 genomes]
rs2295667	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28399971	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34453162	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3895064	1.00[ASN][1000 genomes]
rs4713482	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4713492	1.00[ASN][1000 genomes]
rs4947252	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947329	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4947330	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56662332	0.92[AFR][1000 genomes]
rs59114240	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60149397	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60559550	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60900316	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398259	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7382084	1.00[EUR][1000 genomes]
rs9800604	1.00[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	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
12	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
13	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
14	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
15	nsv884425	chr6:31688518-31698544	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
2	chr6:31682000-31693800	Weak transcription	Fetal Kidney	kidney
3	chr6:31682200-31693400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:31682400-31693600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:31682400-31693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:31682400-31696400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:31683000-31693400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:31683200-31693200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:31683200-31693400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:31683200-31696200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:31683600-31693800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:31684000-31693400	Weak transcription	Fetal Lung	lung
13	chr6:31685800-31696200	Weak transcription	Brain Anterior Caudate	brain
14	chr6:31686200-31693600	Weak transcription	Aorta	Aorta
15	chr6:31686400-31695600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:31686800-31693800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:31686800-31693800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:31686800-31694000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:31686800-31696200	Weak transcription	Small Intestine	intestine
20	chr6:31687000-31693200	Weak transcription	Lung	lung
21	chr6:31687000-31693800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:31687000-31694000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:31687000-31694800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:31687000-31695800	Weak transcription	Pancreas	Pancrea
25	chr6:31687200-31693800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:31687200-31694000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:31687200-31694800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:31687400-31693600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:31687400-31693800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:31688000-31693600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:31688200-31694600	Weak transcription	Gastric	stomach
32	chr6:31688600-31694200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:31688600-31695000	Weak transcription	NHEK	skin
34	chr6:31688800-31693800	Weak transcription	Stomach Mucosa	stomach
35	chr6:31688800-31694200	Strong transcription	Fetal Brain Female	brain
36	chr6:31688800-31695400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:31688800-31696600	Weak transcription	HMEC	breast
38	chr6:31689000-31694600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:31689200-31693400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:31689200-31694800	Strong transcription	Brain Germinal Matrix	brain
41	chr6:31689800-31693400	Weak transcription	NHDF-Ad	bronchial
42	chr6:31689800-31694800	Weak transcription	Esophagus	oesophagus
43	chr6:31689800-31695000	Strong transcription	Fetal Stomach	stomach
44	chr6:31690200-31693600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:31690200-31694000	Weak transcription	Colonic Mucosa	Colon
46	chr6:31690400-31693600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:31690600-31693600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:31690600-31693800	Weak transcription	Liver	Liver
49	chr6:31690800-31693600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:31690800-31693600	Enhancers	K562	blood

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