Variant report

Variant	rs41268884
Chromosome Location	chr6:31553468-31553469
allele	A/G
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	CTCF	chr6:31553411-31553586	GM13976	blood:	n/a	chr6:31553477-31553495
2	CTCF	chr6:31553440-31553590	RPTEC	kidney:	n/a	chr6:31553477-31553495
3	RAD21	chr6:31553359-31553634	GM12878	blood:	n/a	n/a
4	CTCF	chr6:31553400-31553550	HepG2	liver:	n/a	chr6:31553477-31553495
5	SP4	chr6:31553288-31553649	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr6:31553440-31553590	WERI-Rb-1	eye:	n/a	chr6:31553477-31553495
7	CTCF	chr6:31553417-31553551	Medullo	brain:	n/a	chr6:31553477-31553495
8	CTCF	chr6:31553400-31553550	HBMEC	blood vessel:	n/a	chr6:31553477-31553495
9	CTCF	chr6:31553400-31553550	RPTEC	kidney:	n/a	chr6:31553477-31553495
10	CTCF	chr6:31553358-31553592	Fibrobl	skin:	n/a	chr6:31553477-31553495
11	CTCF	chr6:31553380-31553530	GM12873	blood:	n/a	chr6:31553477-31553495
12	CTCF	chr6:31553420-31553570	NB4	blood:	n/a	chr6:31553477-31553495
13	CTCF	chr6:31553400-31553550	AG04449	skin:	n/a	chr6:31553477-31553495
14	CTCF	chr6:31553440-31553590	GM12864	blood:	n/a	chr6:31553477-31553495
15	RAD21	chr6:31553328-31553630	HepG2	liver:	n/a	n/a
16	CTCF	chr6:31553355-31553618	ProgFib	skin:	n/a	chr6:31553477-31553495
17	CTCF	chr6:31553287-31553616	K562	blood:	n/a	chr6:31553477-31553495
18	RCOR1	chr6:31553306-31553657	K562	blood:	n/a	n/a
19	ZNF143	chr6:31553335-31553651	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr6:31553420-31553570	BE2_C	brain:	n/a	chr6:31553477-31553495
21	CTCF	chr6:31553380-31553530	AG09319	gingival:	n/a	chr6:31553477-31553495
22	CTCF	chr6:31553340-31553490	HRE	kidney:	n/a	n/a
23	CTCF	chr6:31553400-31553550	HMEC	breast:	n/a	chr6:31553477-31553495
24	CTCF	chr6:31553400-31553550	HPF	lung:	n/a	chr6:31553477-31553495
25	CTCF	chr6:31553460-31553610	HCM	heart:	n/a	chr6:31553477-31553495
26	CTCF	chr6:31553368-31553631	GM19239	blood:	n/a	chr6:31553477-31553495
27	CTCF	chr6:31553380-31553530	SK-N-SH_RA	brain:	n/a	chr6:31553477-31553495
28	CTCF	chr6:31553355-31553636	GM12878	blood:	n/a	chr6:31553477-31553495
29	CTCF	chr6:31553360-31553510	HA-sp	spinal cord:	n/a	chr6:31553477-31553495
30	CTCF	chr6:31553384-31553613	Hela-S3	cervix:	n/a	chr6:31553477-31553495
31	CTCF	chr6:31553400-31553550	HCFaa	heart:	n/a	chr6:31553477-31553495
32	MAX	chr6:31553448-31553530	K562	blood:	n/a	n/a
33	CTCF	chr6:31553420-31553570	GM12865	blood:	n/a	chr6:31553477-31553495
34	RUNX3	chr6:31553234-31555132	GM12878	blood:	n/a	n/a
35	CTCF	chr6:31553419-31553564	MCF-7	breast:	n/a	chr6:31553477-31553495
36	CTCF	chr6:31553460-31553610	AG10803	skin:	n/a	chr6:31553477-31553495
37	CTCF	chr6:31553440-31553590	HCT-116	colon:	n/a	chr6:31553477-31553495
38	RAD21	chr6:31553261-31553638	HepG2	liver:	n/a	n/a
39	RUNX3	chr6:31553274-31553667	GM12878	blood:	n/a	n/a
40	CTCF	chr6:31553420-31553570	HEK293	kidney:	n/a	chr6:31553477-31553495
41	CTCF	chr6:31553374-31553614	GM13977	blood:	n/a	chr6:31553477-31553495
42	CTCF	chr6:31553440-31553590	HL-60	blood:	n/a	chr6:31553477-31553495
43	CTCF	chr6:31553420-31553570	Hela-S3	cervix:	n/a	chr6:31553477-31553495
44	RAD21	chr6:31553305-31553638	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr6:31553380-31553530	HCM	heart:	n/a	chr6:31553477-31553495
46	POLR2A	chr6:31553276-31555303	GM12891	blood:	n/a	n/a
47	CTCF	chr6:31553440-31553590	GM12865	blood:	n/a	chr6:31553477-31553495
48	CTCF	chr6:31553400-31553550	SK-N-SH_RA	brain:	n/a	chr6:31553477-31553495
49	RAD21	chr6:31553297-31553695	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr6:31553400-31553550	HMF	breast:	n/a	chr6:31553477-31553495

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31553441-31553491	AoSMC	blood vessel:	n/a
2	chr6:31553441-31553491	A549	lung:	n/a
3	chr6:31553441-31553491	HCPEpiC	choroid plexus:	n/a
4	chr6:31553441-31553491	HepG2	liver:	n/a
5	chr6:31553441-31553491	HRCEpiC	kidney:	n/a
6	chr6:31553441-31553491	HMEC	breast:	n/a
7	chr6:31553441-31553491	AG04449	skin:	fetal
8	chr6:31553441-31553491	PrEC	prostate:	n/a
9	chr6:31553441-31553491	BE2_C	brain:	n/a
10	chr6:31553441-31553491	HNPCEpiC	eye:	n/a
11	chr6:31553441-31553491	NHBE	bronchial:	n/a
12	chr6:31553441-31553491	HRE	kidney:	n/a
13	chr6:31553441-31553491	RPTEC	kidney:	n/a
14	chr6:31553441-31553491	GM12892	blood:	n/a
15	chr6:31553441-31553491	AG04450	lung:	fetal
16	chr6:31553441-31553491	GM19239	blood:	n/a
17	chr6:31553441-31553491	LNCaP	prostate:	n/a
18	chr6:31553441-31553491	PFSK-1	brain:	n/a
19	chr6:31553441-31553491	MCF-7	breast:	n/a
20	chr6:31553441-31553491	SK-N-SH_RA	brain:	n/a
21	chr6:31553441-31553491	MCF10A-Er-Src	breast:	n/a
22	chr6:31553441-31553491	AG10803	skin:	n/a
23	chr6:31553441-31553491	SK-N-SH	brain:	n/a
24	chr6:31553441-31553491	NH-A	brain:	n/a
25	chr6:31553441-31553491	NB4	blood:	n/a
26	chr6:31553441-31553491	SAEC	small airway:	n/a
27	chr6:31553441-31553491	SKMC	muscle:	n/a
28	chr6:31553441-31553491	HAEpiC	amniotic membrane:	n/a
29	chr6:31553441-31553491	HRPEpiC	eye:	n/a
30	chr6:31553441-31553491	ECC-1	luminal epithelium:	n/a
31	chr6:31553441-31553491	HEEpiC	esophagus:	n/a
32	chr6:31553441-31553491	HCT-116	colon:	n/a
33	chr6:31553441-31553491	Hela-S3	cervix:	n/a
34	chr6:31553441-31553491	GM06990	blood:	n/a
35	chr6:31553441-31553491	NHDF-neo	bronchial:	n/a
36	chr6:31553441-31553491	ovcar-3	ovarian:	n/a
37	chr6:31553441-31553491	T-47D	breast:	n/a
38	chr6:31553441-31553491	BJ	skin:	n/a
39	chr6:31553441-31553491	HPAEpiC	pulmonary alveolar:	n/a
40	chr6:31553441-31553491	K562	blood:	n/a
41	chr6:31553441-31553491	HCF	heart:	n/a
42	chr6:31553441-31553491	AG09309	skin:	n/a
43	chr6:31553441-31553491	U87	brain:	n/a
44	chr6:31553441-31553491	AG09319	gingival:	n/a
45	chr6:31553441-31553491	HIPEpiC	eye:	n/a
46	chr6:31553441-31553491	HL-60	blood:	n/a
47	chr6:31553441-31553491	PANC-1	pancreas:	n/a
48	chr6:31553441-31553491	SK-N-MC	brain:	n/a
49	chr6:31553441-31553491	IMR90	lung:	fetal
50	chr6:31553441-31553491	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31519280..31519781-chr6:31553143..31553855,2	MCF-7	breast:
2	chr6:31552844..31558545-chr6:31585940..31590373,6	MCF-7	breast:
3	chr6:31511781..31517209-chr6:31545410..31553496,14	K562	blood:
4	chr6:31552082..31553721-chr6:31719786..31722237,2	MCF-7	breast:
5	chr6:31553317..31555989-chr6:31586068..31588677,3	K562	blood:
6	chr6:31553044..31555571-chr6:31558809..31560803,3	K562	blood:
7	chr2:27632384..27633022-chr6:31553212..31553987,2	MCF-7	breast:
8	chr6:31513639..31517977-chr6:31550404..31553496,5	K562	blood:

Variant related genes	Relation type
LST1	TF binding region
LTB	TF binding region
LST1	CpG island
LTB	CpG island
ENSG00000204410	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000115241	Chromatin interaction
ENSG00000213760	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2255798	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2857599	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2857708	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35588235	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41268888	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41268892	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4388309	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31549400-31555600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31549400-31556200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr6:31550000-31553600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:31550000-31553600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:31550000-31553600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:31550000-31554000	Weak transcription	Esophagus	oesophagus
7	chr6:31550000-31555000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:31550000-31556200	Weak transcription	Gastric	stomach
9	chr6:31550000-31583200	Weak transcription	Right Atrium	heart
10	chr6:31550200-31555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:31550200-31556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:31550400-31554600	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:31550800-31553600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:31550800-31553600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:31550800-31560400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:31551000-31553600	Enhancers	Thymus	Thymus
17	chr6:31551000-31554200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:31551000-31554200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:31551000-31554200	Weak transcription	Colonic Mucosa	Colon
20	chr6:31551200-31553600	Enhancers	Fetal Thymus	thymus
21	chr6:31551600-31553600	Enhancers	Primary hematopoietic stem cells	blood
22	chr6:31551800-31553800	Weak transcription	Lung	lung
23	chr6:31552000-31554000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:31552400-31554000	Enhancers	GM12878-XiMat	blood
25	chr6:31552400-31555400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:31552600-31555200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:31552600-31557200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:31552800-31553600	Enhancers	Duodenum Mucosa	Duodenum
29	chr6:31552800-31555200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:31552800-31556000	Enhancers	Dnd41	blood
31	chr6:31553000-31554000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:31553000-31555400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr6:31553000-31556400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr6:31553200-31553600	Enhancers	Adipose Nuclei	Adipose
35	chr6:31553200-31553600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:31553200-31553800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:31553200-31553800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:31553200-31553800	Enhancers	Liver	Liver
39	chr6:31553200-31554200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr6:31553200-31554200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:31553200-31554800	Bivalent Enhancer	Placenta	Placenta
42	chr6:31553200-31555200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:31553200-31555200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr6:31553200-31556600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:31553400-31553600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr6:31553400-31553600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr6:31553400-31553600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:31553400-31553800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr6:31553400-31554200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:31553400-31554200	Enhancers	HUVEC	blood vessel

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