Variant report

Variant	rs3130068
Chromosome Location	chr6:31590354-31590355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31587351-31591130	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:31587203-31590940	SK-N-MC	brain:	n/a	n/a
3	HEY1	chr6:31587125-31591017	K562	blood:	n/a	chr6:31588313-31588328 chr6:31588969-31588984
4	POLR2A	chr6:31590097-31590788	GM12892	blood:	n/a	n/a
5	TEAD4	chr6:31587224-31590369	K562	blood:	n/a	n/a
6	POLR2A	chr6:31587597-31590981	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr6:31590092-31590704	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:31589759-31590562	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:31587263-31591139	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:31590204-31591034	K562	blood:	n/a	n/a
11	POLR2A	chr6:31590248-31591026	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr6:31590285-31590988	K562	blood:	n/a	n/a
13	MXI1	chr6:31587584-31590610	IMR90	lung:	n/a	n/a
14	RFX5	chr6:31587221-31590646	SK-N-SH	brain:	n/a	chr6:31588254-31588263
15	POLR2A	chr6:31590162-31590571	GM12891	blood:	n/a	n/a
16	WRNIP1	chr6:31590353-31590870	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:31587447-31591084	GM12878	blood:	n/a	n/a
18	BHLHE40	chr6:31590321-31590681	K562	blood:	n/a	n/a
19	POLR2A	chr6:31590213-31590420	H1-hESC	embryonic stem cell:	n/a	n/a
20	CUX1	chr6:31590294-31590450	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:31590322-31590862	MCF-7	breast:	n/a	n/a
22	MAX	chr6:31590288-31590838	MCF-7	breast:	n/a	n/a
23	POLR2A	chr6:31590229-31590441	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr6:31590250-31590981	GM12891	blood:	n/a	n/a
25	BHLHE40	chr6:31590351-31590693	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31463965..31465758-chr6:31589334..31591777,2	K562	blood:
2	chr6:31586339..31592286-chr6:31830032..31833457,6	K562	blood:
3	chr6:31552844..31558545-chr6:31585940..31590373,6	MCF-7	breast:
4	chr6:31513053..31519210-chr6:31585987..31595406,29	K562	blood:
5	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
6	chr6:31511829..31516829-chr6:31586761..31590434,8	MCF-7	breast:
7	chr6:31465865..31468194-chr6:31588116..31590521,2	K562	blood:
8	chr6:31463303..31465758-chr6:31589334..31591958,3	K562	blood:
9	chr6:31512646..31517552-chr6:31586243..31590655,20	K562	blood:
10	chr6:31507058..31511692-chr6:31586700..31590601,11	MCF-7	breast:
11	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
12	chr6:31586074..31595285-chr6:31626460..31635395,11	MCF-7	breast:
13	chr6:31542086..31543755-chr6:31589416..31592351,2	K562	blood:
14	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
15	chr6:31546034..31550400-chr6:31586618..31591027,9	K562	blood:
16	chr6:31587220..31590773-chr6:31700977..31706290,6	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA38	TF binding region
PRRC2A	TF binding region
ENSG00000204439	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204482	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204385	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2736177	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2857594	0.87[EUR][1000 genomes]
rs2857600	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2857609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857700	0.87[AMR][1000 genomes]
rs3115668	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115669	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3117578	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130050	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130071	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130625	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131376	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131377	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130068	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31587400-31590400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:31588800-31590400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr6:31588800-31591000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
4	chr6:31589000-31590400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:31589000-31590600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr6:31589000-31590600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:31589000-31591000	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr6:31589200-31590600	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr6:31589200-31590800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:31589200-31591600	Weak transcription	Small Intestine	intestine
11	chr6:31589400-31590400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr6:31589400-31590400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr6:31589400-31590400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr6:31589400-31590600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
15	chr6:31589400-31590600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
16	chr6:31589400-31590600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:31589400-31590600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
18	chr6:31589400-31590600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:31589400-31590600	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr6:31589400-31590600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
21	chr6:31589400-31590600	Flanking Active TSS	Fetal Heart	heart
22	chr6:31589400-31590600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr6:31589400-31590600	Flanking Active TSS	HMEC	breast
24	chr6:31589400-31590600	Flanking Active TSS	HUVEC	blood vessel
25	chr6:31589400-31590800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:31589400-31590800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
27	chr6:31589400-31590800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
28	chr6:31589400-31590800	Transcr. at gene 5' and 3'	K562	blood
29	chr6:31589400-31591000	Transcr. at gene 5' and 3'	NHEK	skin
30	chr6:31589600-31590400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:31589600-31590400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:31589600-31590400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr6:31589600-31590400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:31589600-31590400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:31589600-31590400	Flanking Active TSS	Fetal Brain Male	brain
36	chr6:31589600-31590400	Flanking Active TSS	NH-A	brain
37	chr6:31589600-31590600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
38	chr6:31589600-31590600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:31589600-31590600	Transcr. at gene 5' and 3'	Thymus	Thymus
40	chr6:31589600-31590600	Transcr. at gene 5' and 3'	A549	lung
41	chr6:31589600-31590800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:31589600-31590800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
43	chr6:31589600-31590800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:31589600-31590800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:31589600-31591200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:31589600-31591600	Weak transcription	Ovary	ovary
47	chr6:31589800-31590400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:31589800-31590400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:31589800-31590400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:31589800-31590400	Enhancers	Liver	Liver

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