Variant report

Variant	rs1401419
Chromosome Location	chr11:45879739-45879740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:45878353-45880252	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr11:45879629-45879894	PFSK-1	brain:	n/a	n/a
3	SIN3AK20	chr11:45879684-45879985	SK-N-SH	brain:	n/a	n/a
4	MAFK	chr11:45879495-45880093	IMR90	lung:	n/a	n/a
5	SPI1	chr11:45879570-45879876	GM12878	blood:	n/a	chr11:45879667-45879680 chr11:45879730-45879743 chr11:45879666-45879679 chr11:45879730-45879743
6	TCF12	chr11:45879430-45880078	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:45879730-45879780	HCT-116	colon:	n/a
2	chr11:45879730-45879780	HMEC	breast:	n/a
3	chr11:45879730-45879780	HNPCEpiC	eye:	n/a
4	chr11:45879730-45879780	Caco-2	colon:	n/a
5	chr11:45879730-45879780	HepG2	liver:	n/a
6	chr11:45879730-45879780	BE2_C	brain:	n/a
7	chr11:45879730-45879780	GM12891	blood:	n/a
8	chr11:45879730-45879780	MCF10A-Er-Src	breast:	n/a
9	chr11:45879730-45879780	HEK293	kidney:	embryo
10	chr11:45879730-45879780	PFSK-1	brain:	n/a
11	chr11:45879730-45879780	AG04450	lung:	fetal
12	chr11:45879730-45879780	AG09309	skin:	n/a
13	chr11:45879730-45879780	PrEC	prostate:	n/a
14	chr11:45879730-45879780	ovcar-3	ovarian:	n/a
15	chr11:45879730-45879780	SK-N-MC	brain:	n/a
16	chr11:45879730-45879780	U87	brain:	n/a
17	chr11:45879730-45879780	SKMC	muscle:	n/a
18	chr11:45879730-45879780	PANC-1	pancreas:	n/a
19	chr11:45879730-45879780	HCPEpiC	choroid plexus:	n/a
20	chr11:45879730-45879780	SK-N-SH	brain:	n/a
21	chr11:45879730-45879780	HAEpiC	amniotic membrane:	n/a
22	chr11:45879730-45879780	NHBE	bronchial:	n/a
23	chr11:45879730-45879780	Jurkat	blood:	n/a
24	chr11:45879730-45879780	NB4	blood:	n/a
25	chr11:45879730-45879780	Hela-S3	cervix:	n/a
26	chr11:45879730-45879780	HCF	heart:	n/a
27	chr11:45879730-45879780	HRCEpiC	kidney:	n/a
28	chr11:45879730-45879780	HEEpiC	esophagus:	n/a
29	chr11:45879730-45879780	HRE	kidney:	n/a
30	chr11:45879730-45879780	MCF-7	breast:	n/a
31	chr11:45879730-45879780	AG04449	skin:	fetal
32	chr11:45879730-45879780	SAEC	small airway:	n/a
33	chr11:45879730-45879780	HRPEpiC	eye:	n/a
34	chr11:45879730-45879780	CMK	blood:	n/a
35	chr11:45879730-45879780	IMR90	lung:	fetal
36	chr11:45879730-45879780	Hepatocyte	liver:	n/a
37	chr11:45879730-45879780	H1-hESC	embryonic stem cell:	embryo
38	chr11:45879730-45879780	AG09319	gingival:	n/a
39	chr11:45879730-45879780	HCM	heart:	n/a
40	chr11:45879730-45879780	SK-N-SH_RA	brain:	n/a
41	chr11:45879730-45879780	RPTEC	kidney:	n/a
42	chr11:45879730-45879780	HUVEC	blood vessel:	n/a
43	chr11:45879730-45879780	HPAEpiC	pulmonary alveolar:	n/a
44	chr11:45879730-45879780	LNCaP	prostate:	n/a
45	chr11:45879730-45879780	NT2-D1	testis:	n/a
46	chr11:45879730-45879780	GM06990	blood:	n/a
47	chr11:45879730-45879780	NHDF-neo	bronchial:	n/a
48	chr11:45879730-45879780	HL-60	blood:	n/a
49	chr11:45879730-45879780	GM12878	blood:	n/a
50	chr11:45879730-45879780	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:45867823..45873583-chr11:45876186..45881298,10	MCF-7	breast:
2	chr11:45879680..45881437-chr11:45942342..45944046,2	MCF-7	breast:
3	chr11:45876957..45879799-chr11:46142347..46144267,2	MCF-7	breast:

No data

Variant related genes	Relation type
CRY2	TF binding region
CRY2	CpG island
ENSG00000135365	Chromatin interaction
ENSG00000165905	Chromatin interaction
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10838524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11038672	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11038678	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11038694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11605924	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11607182	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11607883	1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12419690	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12794698	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805422	1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12807179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271845	0.82[YRI][hapmap]
rs34043764	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6485644	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6485645	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6485646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105751	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7112505	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7115753	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7121611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7945565	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7945689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45869800-45883600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45870600-45879800	Weak transcription	Esophagus	oesophagus
3	chr11:45870800-45880800	Weak transcription	HMEC	breast
4	chr11:45872600-45880200	Weak transcription	Aorta	Aorta
5	chr11:45874200-45904200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:45874600-45880000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:45874600-45880000	Weak transcription	Small Intestine	intestine
8	chr11:45875200-45882600	Genic enhancers	Liver	Liver
9	chr11:45875200-45905600	Strong transcription	Primary T cells from cord blood	blood
10	chr11:45875400-45893400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:45875800-45904200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr11:45876400-45904200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:45876600-45882600	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr11:45876600-45882600	Enhancers	Right Atrium	heart
15	chr11:45876800-45879800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:45876800-45881800	Enhancers	Right Ventricle	heart
17	chr11:45876800-45882600	Genic enhancers	Fetal Muscle Leg	muscle
18	chr11:45876800-45882600	Genic enhancers	Fetal Stomach	stomach
19	chr11:45876800-45894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:45876800-45895600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:45876800-45895600	Strong transcription	Thymus	Thymus
22	chr11:45876800-45900200	Strong transcription	Primary B cells from cord blood	blood
23	chr11:45876800-45903600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:45876800-45904600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:45877000-45880000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr11:45877000-45880000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:45877000-45881000	Genic enhancers	Brain Hippocampus Middle	brain
28	chr11:45877000-45885800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:45877000-45885800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:45877000-45885800	Strong transcription	Dnd41	blood
31	chr11:45877000-45885800	Strong transcription	GM12878-XiMat	blood
32	chr11:45877000-45885800	Strong transcription	K562	blood
33	chr11:45877000-45886000	Strong transcription	HepG2	liver
34	chr11:45877000-45893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:45877000-45895600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:45877200-45879800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:45877200-45879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:45877200-45880600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:45877200-45881200	Genic enhancers	NHLF	lung
40	chr11:45877200-45881800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr11:45877200-45882600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:45877200-45883800	Genic enhancers	Left Ventricle	heart
43	chr11:45877200-45886000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:45877200-45893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:45877400-45879800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr11:45877400-45880000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:45877400-45880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr11:45877400-45880800	Strong transcription	Hela-S3	cervix
49	chr11:45877400-45882600	Genic enhancers	Lung	lung
50	chr11:45877400-45887200	Strong transcription	Primary hematopoietic stem cells	blood

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