Variant report

Variant	rs2260050
Chromosome Location	chr6:31591928-31591929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31591125-31592644	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:31591364-31592037	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:31591209-31592615	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:31591166-31592590	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:31591280-31593111	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:31591856-31592482	K562	blood:	n/a	n/a
7	POLR2A	chr6:31591903-31592473	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:31591287-31592551	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr6:31591284-31592527	GM12892	blood:	n/a	n/a
10	HEY1	chr6:31591224-31592577	K562	blood:	n/a	n/a
11	POLR2A	chr6:31591268-31592612	K562	blood:	n/a	n/a
12	POLR2A	chr6:31591219-31592629	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:31591855-31592550	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:31591069-31592539	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:31591210-31592567	PFSK-1	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31586339..31592286-chr6:31830032..31833457,6	K562	blood:
2	chr6:31513053..31519210-chr6:31585987..31595406,29	K562	blood:
3	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
4	chr6:31590578..31592519-chr6:31620452..31622488,2	MCF-7	breast:
5	chr6:31524595..31526236-chr6:31590943..31592445,2	K562	blood:
6	chr6:31463303..31465758-chr6:31589334..31591958,3	K562	blood:
7	chr6:31586074..31595285-chr6:31626460..31635395,11	MCF-7	breast:
8	chr6:31542086..31543755-chr6:31589416..31592351,2	K562	blood:
9	chr6:31513697..31516891-chr6:31590663..31594798,6	K562	blood:
10	chr6:31590485..31592545-chr6:31618288..31620102,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRRC2A	TF binding region
ENSG00000204385	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000234006	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1052486	0.91[ASN][1000 genomes]
rs1077393	0.91[ASN][1000 genomes]
rs13716	0.91[AMR][1000 genomes]
rs2051552	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077491	0.89[ASN][1000 genomes]
rs2077492	0.82[ASN][1000 genomes]
rs2242659	0.82[ASN][1000 genomes]
rs2242660	0.84[ASN][1000 genomes]
rs2259571	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2260000	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2507957	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736155	0.88[ASN][1000 genomes]
rs2736171	0.91[EUR][1000 genomes]
rs2736172	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736176	0.87[AMR][1000 genomes]
rs2736178	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844465	0.82[ASN][1000 genomes]
rs2844472	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844475	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844476	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844477	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2857693	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2857694	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2857697	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2857698	0.87[AMR][1000 genomes]
rs3091280	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3135044	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3993747	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4569	0.81[ASN][1000 genomes]
rs5872	0.87[AMR][1000 genomes]
rs7029	0.81[ASN][1000 genomes]
rs707919	0.87[AMR][1000 genomes]
rs707920	0.81[ASN][1000 genomes]
rs755714	0.91[AMR][1000 genomes]
rs7765613	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7992	0.81[ASN][1000 genomes]
rs805257	0.81[ASN][1000 genomes]
rs805262	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs805299	0.87[AMR][1000 genomes]
rs805301	0.82[ASN][1000 genomes]
rs805302	0.82[ASN][1000 genomes]
rs805303	0.83[ASN][1000 genomes]
rs813115	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
16	nsv884419	chr6:31585000-31632651	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
17	nsv884420	chr6:31586827-31632651	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
18	nsv884421	chr6:31588151-31631907	Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2260050	CSNK2B	Cis_1M	lymphoblastoid	RTeQTL
rs2260050	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2260050	HLA-DQB1	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31589800-31619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31590200-31607000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:31590200-31617600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:31590200-31618800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr6:31590400-31592400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:31590400-31592400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:31590400-31593200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:31590400-31617400	Strong transcription	Rectal Smooth Muscle	rectum
9	chr6:31590400-31617600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:31590400-31618200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr6:31590400-31618600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:31590400-31618600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:31590400-31618600	Strong transcription	Fetal Intestine Small	intestine
14	chr6:31590600-31593000	Weak transcription	Stomach Mucosa	stomach
15	chr6:31590600-31598400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:31590600-31599400	Strong transcription	Psoas Muscle	Psoas
17	chr6:31590600-31601200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr6:31590600-31605000	Strong transcription	A549	lung
19	chr6:31590600-31605200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:31590600-31606200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr6:31590600-31613200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:31590600-31617200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:31590600-31617400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:31590600-31617400	Strong transcription	Right Ventricle	heart
25	chr6:31590600-31617600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:31590600-31617800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr6:31590600-31617800	Strong transcription	Left Ventricle	heart
28	chr6:31590600-31617800	Strong transcription	Thymus	Thymus
29	chr6:31590600-31618000	Strong transcription	Fetal Lung	lung
30	chr6:31590600-31618600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr6:31590600-31618600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:31590600-31618800	Strong transcription	Fetal Stomach	stomach
33	chr6:31590800-31592000	Strong transcription	Adipose Nuclei	Adipose
34	chr6:31590800-31592800	Weak transcription	Fetal Brain Male	brain
35	chr6:31590800-31598800	Strong transcription	HSMM	muscle
36	chr6:31590800-31599600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:31590800-31600600	Strong transcription	Liver	Liver
38	chr6:31590800-31602200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:31590800-31604600	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:31590800-31605600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:31590800-31607000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:31590800-31607000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:31590800-31607200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:31590800-31609200	Strong transcription	Brain Anterior Caudate	brain
45	chr6:31590800-31617400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:31590800-31617600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:31590800-31617800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:31590800-31617800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr6:31590800-31618400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:31590800-31618400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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