Variant report

Variant	rs11211259
Chromosome Location	chr1:46636384-46636385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46636382-46636432	HCF	heart:	n/a
2	chr1:46636382-46636432	HRCEpiC	kidney:	n/a
3	chr1:46636382-46636432	HUVEC	blood vessel:	n/a
4	chr1:46636382-46636432	NB4	blood:	n/a
5	chr1:46636382-46636432	GM06990	blood:	n/a
6	chr1:46636382-46636432	ECC-1	luminal epithelium:	n/a
7	chr1:46636382-46636432	GM19239	blood:	n/a
8	chr1:46636382-46636432	Jurkat	blood:	n/a
9	chr1:46636382-46636432	ProgFib	skin:	n/a
10	chr1:46636382-46636432	HMEC	breast:	n/a
11	chr1:46636382-46636432	PrEC	prostate:	n/a
12	chr1:46636382-46636432	HRPEpiC	eye:	n/a
13	chr1:46636382-46636432	Hela-S3	cervix:	n/a
14	chr1:46636382-46636432	Hepatocyte	liver:	n/a
15	chr1:46636382-46636432	SK-N-MC	brain:	n/a
16	chr1:46636382-46636432	AG09319	gingival:	n/a
17	chr1:46636382-46636432	HPAEpiC	pulmonary alveolar:	n/a
18	chr1:46636382-46636432	HCPEpiC	choroid plexus:	n/a
19	chr1:46636382-46636432	GM12878	blood:	n/a
20	chr1:46636382-46636432	HEK293	kidney:	embryo
21	chr1:46636382-46636432	CMK	blood:	n/a
22	chr1:46636382-46636432	PFSK-1	brain:	n/a
23	chr1:46636382-46636432	SK-N-SH	brain:	n/a
24	chr1:46636382-46636432	K562	blood:	n/a
25	chr1:46636382-46636432	NHBE	bronchial:	n/a
26	chr1:46636382-46636432	NHDF-neo	bronchial:	n/a
27	chr1:46636382-46636432	LNCaP	prostate:	n/a
28	chr1:46636382-46636432	RPTEC	kidney:	n/a
29	chr1:46636382-46636432	AG04449	skin:	fetal
30	chr1:46636382-46636432	AG10803	skin:	n/a
31	chr1:46636382-46636432	Caco-2	colon:	n/a
32	chr1:46636382-46636432	MCF10A-Er-Src	breast:	n/a
33	chr1:46636382-46636432	ovcar-3	ovarian:	n/a
34	chr1:46636382-46636432	A549	lung:	n/a
35	chr1:46636382-46636432	BJ	skin:	n/a
36	chr1:46636382-46636432	BE2_C	brain:	n/a
37	chr1:46636382-46636432	AoSMC	blood vessel:	n/a
38	chr1:46636382-46636432	NT2-D1	testis:	n/a
39	chr1:46636382-46636432	SKMC	muscle:	n/a
40	chr1:46636382-46636432	IMR90	lung:	fetal
41	chr1:46636382-46636432	HNPCEpiC	eye:	n/a
42	chr1:46636382-46636432	T-47D	breast:	n/a
43	chr1:46636382-46636432	HRE	kidney:	n/a
44	chr1:46636382-46636432	HL-60	blood:	n/a
45	chr1:46636382-46636432	PANC-1	pancreas:	n/a
46	chr1:46636382-46636432	AG09309	skin:	n/a
47	chr1:46636382-46636432	U87	brain:	n/a
48	chr1:46636382-46636432	HEEpiC	esophagus:	n/a
49	chr1:46636382-46636432	HAEpiC	amniotic membrane:	n/a
50	chr1:46636382-46636432	HepG2	liver:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46635040..46637380-chr1:46652840..46654559,2	MCF-7	breast:
2	chr1:46634262..46636688-chr1:46646311..46648808,2	MCF-7	breast:
3	chr1:46621624..46623381-chr1:46635953..46637787,2	MCF-7	breast:
4	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
5	chr1:46636028..46638246-chr1:46712360..46714250,2	MCF-7	breast:
6	chr1:46634943..46636544-chr1:46711227..46713970,2	K562	blood:
7	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
8	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
9	chr1:46619572..46621835-chr1:46635358..46637893,2	MCF-7	breast:
10	chr1:46636119..46638195-chr2:81815588..81817410,2	MCF-7	breast:
11	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
12	chr1:46630846..46632404-chr1:46635981..46638710,2	K562	blood:

No data

Variant related genes	Relation type
TSPAN1	CpG island
ENSG00000227857	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10493121	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211258	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029005	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12029134	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12029936	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064594	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134419	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618281	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1620877	0.88[ASN][1000 genomes]
rs3753363	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3820082	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3845300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845301	0.82[ASN][1000 genomes]
rs6661071	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686661	0.82[ASN][1000 genomes]
rs7512966	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536272	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs785475	0.82[AMR][1000 genomes]
rs785476	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46633200-46636800	Weak transcription	Placenta	Placenta
2	chr1:46633200-46636800	Weak transcription	HUVEC	blood vessel
3	chr1:46633200-46637000	Weak transcription	Esophagus	oesophagus
4	chr1:46633200-46637000	Weak transcription	Pancreas	Pancrea
5	chr1:46633200-46637000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:46633200-46637600	Weak transcription	Psoas Muscle	Psoas
7	chr1:46633400-46636800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:46633400-46636800	Weak transcription	GM12878-XiMat	blood
9	chr1:46633400-46637200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:46633400-46637800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:46634000-46636800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:46634400-46636800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:46634400-46638800	Weak transcription	K562	blood
19	chr1:46634800-46636800	Weak transcription	Fetal Thymus	thymus
20	chr1:46635600-46636800	Enhancers	Adipose Nuclei	Adipose
21	chr1:46635600-46636800	Weak transcription	Right Ventricle	heart
22	chr1:46635600-46642200	Enhancers	Lung	lung
23	chr1:46635800-46636800	Weak transcription	Gastric	stomach
24	chr1:46635800-46636800	Weak transcription	Left Ventricle	heart
25	chr1:46635800-46636800	Weak transcription	Right Atrium	heart
26	chr1:46635800-46636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:46635800-46636800	Weak transcription	Spleen	Spleen

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