Variant report

Variant	rs1116221
Chromosome Location	chr6:30071330-30071331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:122)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:30070810-30071409	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr6:30070653-30071428	MCF-7	breast:	n/a	n/a
3	CTCF	chr6:30071280-30071430	HEK293	kidney:	n/a	n/a
4	RAD21	chr6:30070729-30071414	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr6:30070810-30071359	IMR90	lung:	n/a	n/a
6	SMC3	chr6:30070631-30071462	SK-N-SH	brain:	n/a	n/a
7	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
8	USF2	chr6:30071330-30071333	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr6:30070600-30071433	HCT-116	colon:	n/a	n/a
10	MAX	chr6:30070774-30071764	H1-hESC	embryonic stem cell:	n/a	n/a
11	SPI1	chr6:30070630-30071431	GM12878	blood:	n/a	n/a
12	CTCF	chr6:30070693-30071444	MCF-7	breast:	n/a	n/a
13	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
14	CTCF	chr6:30071244-30071333	MCF-7	breast:	n/a	n/a
15	FOXA2	chr6:30070782-30071341	A549	lung:	n/a	n/a
16	RAD21	chr6:30070545-30071451	HCT-116	colon:	n/a	n/a
17	CTCF	chr6:30070745-30071373	K562	blood:	n/a	n/a
18	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
19	POLR2A	chr6:30068290-30071350	HepG2	liver:	n/a	n/a
20	CTCF	chr6:30070742-30071384	HCT-116	colon:	n/a	n/a
21	WRNIP1	chr6:30070888-30071450	GM12878	blood:	n/a	n/a
22	MAX	chr6:30070848-30071561	H1-hESC	embryonic stem cell:	n/a	n/a
23	SMC3	chr6:30070713-30071455	HepG2	liver:	n/a	n/a
24	MAX	chr6:30070817-30071604	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr6:30071204-30071398	MCF-7	breast:	n/a	n/a
26	MAX	chr6:30070895-30071497	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr6:30070819-30071357	GM12878	blood:	n/a	n/a
28	MXI1	chr6:30070914-30071558	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr6:30070806-30071336	GM12878	blood:	n/a	n/a
30	RAD21	chr6:30070507-30071879	SK-N-SH	brain:	n/a	n/a
31	MAX	chr6:30070752-30071337	K562	blood:	n/a	n/a
32	CBX3	chr6:30070665-30071505	K562	blood:	n/a	n/a
33	CTCF	chr6:30071225-30071349	MCF-7	breast:	n/a	n/a
34	MAX	chr6:30070852-30071519	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr6:30071293-30071336	GM10248	blood:	n/a	n/a
36	NFIC	chr6:30070711-30071516	HepG2	liver:	n/a	n/a
37	MAZ	chr6:30069160-30071487	IMR90	lung:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
38	POLR2A	chr6:30071046-30071458	MCF-7	breast:	n/a	n/a
39	MAX	chr6:30070725-30071612	MCF-7	breast:	n/a	n/a
40	TCF12	chr6:30070660-30071430	A549	lung:	n/a	n/a
41	RAD21	chr6:30070718-30071424	HepG2	liver:	n/a	n/a
42	CTCF	chr6:30070233-30071526	HCT-116	colon:	n/a	n/a
43	RAD21	chr6:30070708-30071492	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr6:30069267-30071939	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr6:30070797-30071343	HepG2	liver:	n/a	n/a
46	RAD21	chr6:30070772-30071336	SK-N-SH_RA	brain:	n/a	n/a
47	SMC3	chr6:30070810-30071429	GM12878	blood:	n/a	n/a
48	HDAC2	chr6:30070783-30071410	HepG2	liver:	n/a	n/a
49	CTCF	chr6:30071280-30071430	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr6:30071247-30071370	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30071288-30071338	GM12892	blood:	n/a
2	chr6:30071295-30071345	SK-N-SH	brain:	n/a
3	chr6:30071288-30071338	ProgFib	skin:	n/a
4	chr6:30071288-30071338	SAEC	small airway:	n/a
5	chr6:30071288-30071338	T-47D	breast:	n/a
6	chr6:30071295-30071345	ProgFib	skin:	n/a
7	chr6:30071295-30071345	MCF-7	breast:	n/a
8	chr6:30071288-30071338	GM06990	blood:	n/a
9	chr6:30071295-30071345	SK-N-SH_RA	brain:	n/a
10	chr6:30071295-30071345	K562	blood:	n/a
11	chr6:30071288-30071338	PFSK-1	brain:	n/a
12	chr6:30071288-30071338	Jurkat	blood:	n/a
13	chr6:30071295-30071345	HRE	kidney:	n/a
14	chr6:30071288-30071338	Caco-2	colon:	n/a
15	chr6:30071295-30071345	RPTEC	kidney:	n/a
16	chr6:30071288-30071338	GM12878	blood:	n/a
17	chr6:30071288-30071338	GM12891	blood:	n/a
18	chr6:30071295-30071345	AG04450	lung:	fetal
19	chr6:30071295-30071345	ovcar-3	ovarian:	n/a
20	chr6:30071295-30071345	Hela-S3	cervix:	n/a
21	chr6:30071295-30071345	AG09319	gingival:	n/a
22	chr6:30071295-30071345	NB4	blood:	n/a
23	chr6:30071295-30071345	SAEC	small airway:	n/a
24	chr6:30071295-30071345	NHDF-neo	bronchial:	n/a
25	chr6:30071295-30071345	GM12892	blood:	n/a
26	chr6:30071295-30071345	HIPEpiC	eye:	n/a
27	chr6:30071288-30071338	HL-60	blood:	n/a
28	chr6:30071295-30071345	IMR90	lung:	fetal
29	chr6:30071288-30071338	SK-N-SH_RA	brain:	n/a
30	chr6:30071288-30071338	BJ	skin:	n/a
31	chr6:30071288-30071338	NT2-D1	testis:	n/a
32	chr6:30071295-30071345	H1-hESC	embryonic stem cell:	embryo
33	chr6:30071295-30071345	NHBE	bronchial:	n/a
34	chr6:30071288-30071338	HMEC	breast:	n/a
35	chr6:30071288-30071338	IMR90	lung:	fetal
36	chr6:30071288-30071338	GM19239	blood:	n/a
37	chr6:30071295-30071345	ECC-1	luminal epithelium:	n/a
38	chr6:30071288-30071338	H1-hESC	embryonic stem cell:	embryo
39	chr6:30071295-30071345	HL-60	blood:	n/a
40	chr6:30071295-30071345	AoSMC	blood vessel:	n/a
41	chr6:30071295-30071345	HCF	heart:	n/a
42	chr6:30071295-30071345	HUVEC	blood vessel:	n/a
43	chr6:30071295-30071345	HepG2	liver:	n/a
44	chr6:30071288-30071338	Hepatocyte	liver:	n/a
45	chr6:30071288-30071338	K562	blood:	n/a
46	chr6:30071288-30071338	NHBE	bronchial:	n/a
47	chr6:30071295-30071345	SK-N-MC	brain:	n/a
48	chr6:30071295-30071345	AG09309	skin:	n/a
49	chr6:30071288-30071338	LNCaP	prostate:	n/a
50	chr6:30071288-30071338	HIPEpiC	eye:	n/a

(count:16 , 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	chr6:30071292..30074099-chr6:30075439..30077084,2	K562	blood:
4	chr6:30039673..30045870-chr6:30065915..30071954,9	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	chr6:30043377..30045110-chr6:30070275..30072110,2	MCF-7	breast:
12	chr6:30070612..30071430-chr6:30098763..30099444,2	MCF-7	breast:
13	chr6:30070557..30071542-chr6:30364602..30365386,4	K562	blood:
14	chr6:30071030..30071601-chr6:30135445..30136152,2	MCF-7	breast:
15	chr6:30070471..30072023-chr6:30098513..30099477,20	MCF-7	breast:
16	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM31-1	chr6:30071249-30071566	NONHSAT108598

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000204625	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1116222	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248289	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524005	0.86[CEU][hapmap]
rs2844796	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1116221	HIST1H3J	cis	parietal	SCAN
rs1116221	ZNF323	cis	parietal	SCAN
rs1116221	ZSCAN23	cis	parietal	SCAN
rs1116221	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1116221	ABT1	cis	parietal	SCAN
rs1116221	Hs.519979	cis	multi-tissue	Pritchard
rs1116221	HIST1H2AM	cis	parietal	SCAN
rs1116221	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
6	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
7	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr6:30069600-30071400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:30069600-30071400	Active TSS	Psoas Muscle	Psoas
10	chr6:30069600-30071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:30069800-30071800	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:30070000-30071600	Flanking Active TSS	K562	blood
13	chr6:30070000-30071800	Enhancers	Spleen	Spleen
14	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:30070200-30071400	Flanking Active TSS	Hela-S3	cervix
16	chr6:30070200-30071800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr6:30070400-30071400	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr6:30070400-30071600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:30070400-30071600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:30070400-30071600	Bivalent Enhancer	Dnd41	blood
21	chr6:30070400-30071800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr6:30070800-30071400	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr6:30070800-30071400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr6:30070800-30071400	Flanking Active TSS	GM12878-XiMat	blood
25	chr6:30070800-30071400	Flanking Bivalent TSS/Enh	NH-A	brain
26	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
27	chr6:30070800-30071600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr6:30070800-30071600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:30070800-30071600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:30070800-30071600	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
32	chr6:30070800-30071600	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr6:30070800-30072000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:30071000-30071400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:30071000-30071400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:30071000-30071400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:30071000-30071400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:30071000-30071400	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:30071000-30071400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr6:30071000-30071400	Active TSS	Colonic Mucosa	Colon
41	chr6:30071000-30071400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr6:30071000-30071400	Active TSS	Lung	lung
43	chr6:30071000-30071400	Active TSS	A549	lung
44	chr6:30071000-30071400	Flanking Active TSS	NHLF	lung
45	chr6:30071000-30071400	Active TSS	Osteobl	bone
46	chr6:30071000-30071600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr6:30071000-30071600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
48	chr6:30071000-30071600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:30071000-30071600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:30071000-30071600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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