Variant report

Variant	rs2240070
Chromosome Location	chr6:30071110-30071111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:269)
CpG islands
(count:122)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:269 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr6:30070880-30071323	GM12878	blood:	n/a	n/a
2	RAD21	chr6:30070822-30071205	SK-N-SH_RA	brain:	n/a	n/a
3	YY1	chr6:30070783-30071287	HepG2	liver:	n/a	n/a
4	RAD21	chr6:30070810-30071409	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr6:30070758-30071326	U2OS	brain:	n/a	n/a
6	CTCF	chr6:30070960-30071110	K562	blood:	n/a	n/a
7	ZKSCAN1	chr6:30070865-30071125	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr6:30070653-30071428	MCF-7	breast:	n/a	n/a
9	FOXP2	chr6:30070865-30071208	SK-N-MC	brain:	n/a	n/a
10	RAD21	chr6:30070729-30071414	ECC-1	luminal epithelium:	n/a	n/a
11	GABPA	chr6:30070823-30071180	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr6:30070810-30071359	IMR90	lung:	n/a	n/a
13	POLR2A	chr6:30070727-30071175	HCT-116	colon:	n/a	n/a
14	SP4	chr6:30070858-30071192	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr6:30070960-30071110	HEEpiC	esophagus:	n/a	n/a
16	MAZ	chr6:30070820-30071248	K562	blood:	n/a	n/a
17	JUND	chr6:30070881-30071171	H1-hESC	embryonic stem cell:	n/a	n/a
18	SMC3	chr6:30070631-30071462	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr6:30070856-30071192	GM19240	blood:	n/a	n/a
20	TBL1XR1	chr6:30070907-30071172	GM12878	blood:	n/a	n/a
21	STAT3	chr6:30070856-30071128	GM12878	blood:	n/a	n/a
22	CTCF	chr6:30070872-30071148	MCF-7	breast:	n/a	n/a
23	CTCF	chr6:30070877-30071162	GM10266	blood:	n/a	n/a
24	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
25	FOXA2	chr6:30070786-30071158	HepG2	liver:	n/a	n/a
26	CTCF	chr6:30070960-30071110	SK-N-SH_RA	brain:	n/a	n/a
27	RAD21	chr6:30070600-30071433	HCT-116	colon:	n/a	n/a
28	MAX	chr6:30070774-30071764	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:30070980-30071130	GM12873	blood:	n/a	n/a
30	ELF1	chr6:30070755-30071188	HepG2	liver:	n/a	chr6:30071007-30071020
31	FOXA1	chr6:30070820-30071209	T-47D	breast:	n/a	n/a
32	RAD21	chr6:30070805-30071234	GM12878	blood:	n/a	n/a
33	FOXA1	chr6:30070827-30071167	T-47D	breast:	n/a	n/a
34	CTCF	chr6:30070853-30071182	GM12878	blood:	n/a	n/a
35	MAX	chr6:30070850-30071181	NB4	blood:	n/a	n/a
36	ELK1	chr6:30070886-30071141	GM12878	blood:	n/a	n/a
37	CTCF	chr6:30070960-30071110	HRE	kidney:	n/a	n/a
38	CTCF	chr6:30070881-30071157	Kidney_OC	kidney:	n/a	n/a
39	CTCF	chr6:30070861-30071297	GM12891	blood:	n/a	n/a
40	CTCF	chr6:30070960-30071110	GM12866	blood:	n/a	n/a
41	SPI1	chr6:30070630-30071431	GM12878	blood:	n/a	n/a
42	MYC	chr6:30070823-30071229	K562	blood:	n/a	n/a
43	RAD21	chr6:30070846-30071197	A549	lung:	n/a	n/a
44	CTCF	chr6:30070980-30071130	GM12867	blood:	n/a	n/a
45	CTCF	chr6:30070825-30071174	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr6:30070693-30071444	MCF-7	breast:	n/a	n/a
47	FOXA1	chr6:30070643-30071249	HepG2	liver:	n/a	n/a
48	CTCF	chr6:30070857-30071150	GM13977	blood:	n/a	n/a
49	JUN	chr6:30070891-30071135	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZNF143	chr6:30070848-30071171	Hela-S3	cervix:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30071060-30071110	ovcar-3	ovarian:	n/a
2	chr6:30071060-30071110	AG09319	gingival:	n/a
3	chr6:30071067-30071117	Caco-2	colon:	n/a
4	chr6:30071067-30071117	HCF	heart:	n/a
5	chr6:30071067-30071117	ProgFib	skin:	n/a
6	chr6:30071060-30071110	SK-N-MC	brain:	n/a
7	chr6:30071060-30071110	MCF10A-Er-Src	breast:	n/a
8	chr6:30071067-30071117	HCPEpiC	choroid plexus:	n/a
9	chr6:30071060-30071110	HIPEpiC	eye:	n/a
10	chr6:30071067-30071117	HIPEpiC	eye:	n/a
11	chr6:30071060-30071110	SK-N-SH_RA	brain:	n/a
12	chr6:30071060-30071110	HRE	kidney:	n/a
13	chr6:30071067-30071117	ECC-1	luminal epithelium:	n/a
14	chr6:30071060-30071110	ECC-1	luminal epithelium:	n/a
15	chr6:30071060-30071110	HEK293	kidney:	embryo
16	chr6:30071060-30071110	HAEpiC	amniotic membrane:	n/a
17	chr6:30071067-30071117	AG09319	gingival:	n/a
18	chr6:30071067-30071117	CMK	blood:	n/a
19	chr6:30071060-30071110	A549	lung:	n/a
20	chr6:30071067-30071117	NT2-D1	testis:	n/a
21	chr6:30071060-30071110	AG04449	skin:	fetal
22	chr6:30071067-30071117	HUVEC	blood vessel:	n/a
23	chr6:30071067-30071117	ovcar-3	ovarian:	n/a
24	chr6:30071060-30071110	PANC-1	pancreas:	n/a
25	chr6:30071067-30071117	HMEC	breast:	n/a
26	chr6:30071060-30071110	LNCaP	prostate:	n/a
27	chr6:30071067-30071117	NH-A	brain:	n/a
28	chr6:30071060-30071110	HCPEpiC	choroid plexus:	n/a
29	chr6:30071060-30071110	BJ	skin:	n/a
30	chr6:30071067-30071117	NB4	blood:	n/a
31	chr6:30071067-30071117	NHDF-neo	bronchial:	n/a
32	chr6:30071067-30071117	HNPCEpiC	eye:	n/a
33	chr6:30071067-30071117	HRCEpiC	kidney:	n/a
34	chr6:30071067-30071117	Hela-S3	cervix:	n/a
35	chr6:30071067-30071117	BJ	skin:	n/a
36	chr6:30071067-30071117	HEEpiC	esophagus:	n/a
37	chr6:30071067-30071117	MCF10A-Er-Src	breast:	n/a
38	chr6:30071060-30071110	AG04450	lung:	fetal
39	chr6:30071067-30071117	Hepatocyte	liver:	n/a
40	chr6:30071060-30071110	Caco-2	colon:	n/a
41	chr6:30071067-30071117	RPTEC	kidney:	n/a
42	chr6:30071067-30071117	GM06990	blood:	n/a
43	chr6:30071067-30071117	U87	brain:	n/a
44	chr6:30071060-30071110	PrEC	prostate:	n/a
45	chr6:30071067-30071117	PANC-1	pancreas:	n/a
46	chr6:30071067-30071117	HepG2	liver:	n/a
47	chr6:30071060-30071110	HEEpiC	esophagus:	n/a
48	chr6:30071067-30071117	AoSMC	blood vessel:	n/a
49	chr6:30071060-30071110	NB4	blood:	n/a
50	chr6:30071067-30071117	AG10803	skin:	n/a

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30070301..30072986-chr6:30097734..30100221,43	MCF-7	breast:
2	chr6:30070449..30072089-chr6:30137197..30138565,6	MCF-7	breast:
3	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr6:30070520..30071450-chr6:30137404..30138412,4	MCF-7	breast:
6	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
7	chr6:30070766..30071459-chr6:30135056..30135745,2	K562	blood:
8	chr6:30070544..30071580-chr6:30137122..30138246,6	K562	blood:
9	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
10	chr6:30070180..30072059-chr6:30098450..30099535,14	K562	blood:
11	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
12	chr6:30043377..30045110-chr6:30070275..30072110,2	MCF-7	breast:
13	chr6:30070612..30071430-chr6:30098763..30099444,2	MCF-7	breast:
14	chr6:30042922..30044278-chr6:30069878..30071198,4	MCF-7	breast:
15	chr6:30070557..30071542-chr6:30364602..30365386,4	K562	blood:
16	chr6:30071030..30071601-chr6:30135445..30136152,2	MCF-7	breast:
17	chr6:30070471..30072023-chr6:30098513..30099477,20	MCF-7	breast:
18	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
19	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000234127	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204625	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000252901	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3094136	0.83[EUR][1000 genomes]
rs3132680	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457150	0.80[EUR][1000 genomes]
rs6904455	0.86[AFR][1000 genomes]
rs9261395	0.92[AFR][1000 genomes]
rs9261401	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2240070	HLA-L	cis	lymphoblastoid	seeQTL
rs2240070	HIST1H2AM	cis	parietal	SCAN
rs2240070	HCG22	cis	lymphoblastoid	seeQTL
rs2240070	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
3	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
7	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
8	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr6:30069600-30071200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:30069600-30071200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:30069600-30071400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:30069600-30071400	Active TSS	Psoas Muscle	Psoas
13	chr6:30069600-30071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:30069800-30071200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:30069800-30071200	Active TSS	Brain Anterior Caudate	brain
16	chr6:30069800-30071200	Active TSS	Brain Substantia Nigra	brain
17	chr6:30069800-30071200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:30069800-30071800	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:30070000-30071200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:30070000-30071600	Flanking Active TSS	K562	blood
21	chr6:30070000-30071800	Enhancers	Spleen	Spleen
22	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:30070200-30071200	Active TSS	Right Ventricle	heart
24	chr6:30070200-30071400	Flanking Active TSS	Hela-S3	cervix
25	chr6:30070200-30071800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr6:30070400-30071200	Active TSS	Right Atrium	heart
27	chr6:30070400-30071400	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr6:30070400-30071600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:30070400-30071600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:30070400-30071600	Bivalent Enhancer	Dnd41	blood
31	chr6:30070400-30071800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr6:30070600-30071200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:30070800-30071200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:30070800-30071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:30070800-30071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:30070800-30071200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:30070800-30071200	Bivalent Enhancer	Fetal Heart	heart
38	chr6:30070800-30071200	Flanking Active TSS	HUVEC	blood vessel
39	chr6:30070800-30071400	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr6:30070800-30071400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr6:30070800-30071400	Flanking Active TSS	GM12878-XiMat	blood
42	chr6:30070800-30071400	Flanking Bivalent TSS/Enh	NH-A	brain
43	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr6:30070800-30071600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr6:30070800-30071600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:30070800-30071600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr6:30070800-30071600	Bivalent/Poised TSS	Fetal Kidney	kidney
48	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Thymus	Thymus
50	chr6:30070800-30072000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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