Variant report

Variant	rs11961270
Chromosome Location	chr6:35575378-35575379
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	chr6:35575325-35575573	A549	lung:	n/a	n/a
2	POLR2A	chr6:35575195-35575469	K562	blood:	n/a	n/a
3	POLR2A	chr6:35575197-35575702	K562	blood:	n/a	n/a
4	POLR2A	chr6:35575249-35575515	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000218749	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11963040	1.00[YRI][hapmap]
rs11963207	0.85[AFR][1000 genomes]
rs11964534	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11967862	1.00[YRI][hapmap]
rs11969602	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6457832	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6917044	1.00[YRI][hapmap]
rs7749799	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7771718	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1031987	chr6:35476562-35579375	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv462913	chr6:35502202-35592744	Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv602923	chr6:35502202-35592744	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv517211	chr6:35502202-35607571	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1017625	chr6:35505311-35576552	Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1019593	chr6:35505311-35579375	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv1022049	chr6:35506731-35576552	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1025296	chr6:35507179-35579375	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv885801	chr6:35537406-35671651	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35545000-35601800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:35558600-35580400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:35565400-35579800	Weak transcription	Ovary	ovary
4	chr6:35569200-35575400	Weak transcription	K562	blood
5	chr6:35569400-35591600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:35569600-35587800	Weak transcription	Placenta	Placenta
7	chr6:35570200-35608600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:35570600-35575400	Weak transcription	Colonic Mucosa	Colon
9	chr6:35570600-35575400	Weak transcription	Gastric	stomach
10	chr6:35570600-35577400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:35570600-35578600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:35570600-35578600	Weak transcription	Fetal Brain Male	brain
13	chr6:35570600-35579000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:35570600-35580000	Weak transcription	Small Intestine	intestine
15	chr6:35570600-35583400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:35570600-35587800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:35570800-35575400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:35570800-35579000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:35570800-35579000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:35570800-35580000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:35570800-35585200	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:35570800-35586000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:35570800-35586200	Weak transcription	Fetal Stomach	stomach
24	chr6:35570800-35586200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:35570800-35611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:35571000-35575400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:35571000-35580400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:35571000-35582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:35571000-35590600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:35571000-35602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:35571200-35578800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:35571200-35580000	Weak transcription	Adipose Nuclei	Adipose
33	chr6:35571200-35580000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:35571200-35580200	Weak transcription	Primary B cells from cord blood	blood
35	chr6:35571200-35585400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:35571200-35587200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:35571200-35611800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:35571400-35581400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:35571400-35587200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:35571600-35575400	Weak transcription	Brain Anterior Caudate	brain
41	chr6:35571600-35578400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:35571600-35578800	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:35571800-35583000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:35571800-35583400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:35572000-35578600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:35572000-35578600	Weak transcription	Aorta	Aorta
47	chr6:35572000-35578800	Weak transcription	Fetal Heart	heart
48	chr6:35572000-35579600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:35572000-35581600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:35572000-35584800	Weak transcription	Brain Angular Gyrus	brain

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