Variant report

Variant	rs1492481
Chromosome Location	chr3:111856024-111856025
allele	A/C
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	RAD21	chr3:111856007-111856239	SK-N-SH_RA	brain:	n/a	n/a
2	SMC3	chr3:111855988-111856298	HepG2	liver:	n/a	n/a
3	RAD21	chr3:111855730-111856392	GM12878	blood:	n/a	n/a
4	ATF2	chr3:111854493-111856546	GM12878	blood:	n/a	n/a
5	CHD1	chr3:111854607-111856268	GM12878	blood:	n/a	n/a
6	RAD21	chr3:111855977-111856339	A549	lung:	n/a	n/a
7	RAD21	chr3:111855677-111856437	GM12878	blood:	n/a	n/a
8	CEBPB	chr3:111854430-111856554	GM12878	blood:	n/a	n/a
9	CTCF	chr3:111856014-111856267	Hela-S3	cervix:	n/a	chr3:111856137-111856153
10	CTCF	chr3:111855701-111856283	H1-hESC	embryonic stem cell:	n/a	chr3:111856137-111856153
11	RFX5	chr3:111855706-111856496	GM12878	blood:	n/a	chr3:111856465-111856478
12	CTCF	chr3:111855911-111856235	A549	lung:	n/a	chr3:111856137-111856153
13	EBF1	chr3:111851012-111856368	GM12878	blood:	n/a	chr3:111852245-111852256
14	TCF7L2	chr3:111855912-111856450	HEK293	kidney:	n/a	n/a
15	CTCF	chr3:111855970-111856321	IMR90	lung:	n/a	chr3:111856137-111856153
16	PML	chr3:111854348-111856637	GM12878	blood:	n/a	n/a
17	CTCF	chr3:111856010-111856251	GM10248	blood:	n/a	chr3:111856137-111856153
18	GTF2F1	chr3:111855709-111856168	H1-hESC	embryonic stem cell:	n/a	n/a
19	BCLAF1	chr3:111855436-111856569	GM12878	blood:	n/a	n/a
20	MEF2A	chr3:111855731-111856561	GM12878	blood:	n/a	chr3:111856250-111856265 chr3:111856249-111856265 chr3:111856246-111856267 chr3:111856253-111856262 chr3:111856246-111856267 chr3:111856252-111856263 chr3:111856500-111856517
21	EP300	chr3:111855739-111856408	GM12878	blood:	n/a	n/a
22	MYC	chr3:111855869-111856228	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr3:111855659-111856166	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr3:111856020-111856170	AG04450	lung:	n/a	chr3:111856137-111856153
25	RAD21	chr3:111855712-111856455	GM12878	blood:	n/a	n/a
26	CTCF	chr3:111855801-111856334	K562	blood:	n/a	chr3:111856137-111856153
27	MAX	chr3:111855627-111856234	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr3:111855990-111856275	Spleen_OC	spleen:	n/a	chr3:111856137-111856153
29	CTCF	chr3:111856019-111856252	LNCaP	prostate:	n/a	chr3:111856137-111856153
30	STAT1	chr3:111855706-111856173	GM12878	blood:	n/a	n/a
31	RAD21	chr3:111855731-111856472	HCT-116	colon:	n/a	n/a
32	RUNX3	chr3:111855671-111856417	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:111855613-111856183	GM12891	blood:	n/a	n/a
34	TBP	chr3:111854620-111856510	GM12878	blood:	n/a	n/a
35	YY1	chr3:111855677-111856258	GM12878	blood:	n/a	n/a
36	RAD21	chr3:111855726-111856324	H1-hESC	embryonic stem cell:	n/a	n/a
37	SMC3	chr3:111855834-111856301	SK-N-SH	brain:	n/a	n/a
38	E2F4	chr3:111855659-111856205	GM12878	blood:	n/a	n/a
39	USF2	chr3:111855862-111856153	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:111856004-111856234	MCF-7	breast:	n/a	chr3:111856137-111856153
41	CTCF	chr3:111855999-111856309	A549	lung:	n/a	chr3:111856137-111856153
42	CTCF	chr3:111855989-111856185	A549	lung:	n/a	chr3:111856137-111856153
43	FOXM1	chr3:111855532-111856441	GM12878	blood:	n/a	n/a
44	NFIC	chr3:111853158-111857194	GM12878	blood:	n/a	n/a
45	CTCF	chr3:111856002-111856289	HUVEC	blood vessel:	n/a	chr3:111856137-111856153
46	MAX	chr3:111855723-111856202	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:111855711-111856179	GM12891	blood:	n/a	n/a
48	NFATC1	chr3:111854635-111856346	GM12878	blood:	n/a	n/a
49	MAX	chr3:111855683-111856393	GM12878	blood:	n/a	chr3:111856381-111856388
50	HDAC2	chr3:111855714-111856078	H1-hESC	embryonic stem cell:	n/a	chr3:111855752-111855766 chr3:111855751-111855765 chr3:111855754-111855768

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111855697..111856656-chr3:112238008..112238836,2	K562	blood:
2	chr3:111851024..111853542-chr3:111855899..111858560,2	K562	blood:

Variant related genes	Relation type
GCSAM	TF binding region
ENSG00000261488	Chromatin interaction
ENSG00000174500	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10511306	0.94[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511307	0.94[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511308	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs10934156	0.92[YRI][hapmap]
rs11919901	0.92[YRI][hapmap]
rs11924882	0.92[YRI][hapmap]
rs11926448	0.83[AFR][1000 genomes]
rs11928130	0.94[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053863	0.88[CEU][hapmap]
rs13059342	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs13061801	0.82[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs13069933	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077603	0.92[YRI][hapmap]
rs13078713	0.91[YRI][hapmap]
rs13080696	0.81[AFR][1000 genomes]
rs13087387	0.92[YRI][hapmap]
rs13089316	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs13090344	0.92[YRI][hapmap]
rs1388855	0.94[CEU][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492480	0.94[ASN][1000 genomes]
rs1492483	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492484	0.94[CEU][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492485	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492486	0.89[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586874	0.92[YRI][hapmap]
rs1602672	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1948404	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs1994772	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029638	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34043603	0.83[AFR][1000 genomes]
rs35411358	0.87[EUR][1000 genomes]
rs4279069	0.85[YRI][hapmap]
rs4564948	0.80[CEU][hapmap];0.92[YRI][hapmap]
rs4682100	0.92[YRI][hapmap]
rs4682389	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs6781137	0.82[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs7651558	0.93[ASN][1000 genomes]
rs879652	0.94[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950528	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111848200-111857000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:111848400-111856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:111852200-111857000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:111852200-111857600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:111852200-111863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:111852400-111856200	Enhancers	Fetal Thymus	thymus
7	chr3:111852400-111856200	Enhancers	Thymus	Thymus
8	chr3:111852400-111856600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:111852400-111856600	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:111852400-111857000	Enhancers	Primary B cells from cord blood	blood
11	chr3:111852400-111857200	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:111852600-111856600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:111852600-111857600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:111852800-111856600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:111853000-111856200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:111853000-111856400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:111853200-111856200	Enhancers	Primary T cells from cord blood	blood
18	chr3:111853200-111857000	Enhancers	Stomach Mucosa	stomach
19	chr3:111853400-111867400	Weak transcription	Gastric	stomach
20	chr3:111853600-111856400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:111853600-111857000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:111853800-111857000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:111854200-111856400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:111854200-111856800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:111854200-111857000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:111854600-111856400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:111854600-111857000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:111854600-111858000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:111854800-111856200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:111854800-111857600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:111854800-111857800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:111855000-111857400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:111855000-111857600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:111855000-111858000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:111855200-111858000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:111855400-111856800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:111855400-111857000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:111855400-111857600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:111855400-111858000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:111855600-111856200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:111855600-111856200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:111855600-111856200	Enhancers	Brain Cingulate Gyrus	brain
43	chr3:111855600-111856400	Enhancers	Brain Angular Gyrus	brain
44	chr3:111855600-111856600	Enhancers	Brain Substantia Nigra	brain
45	chr3:111855600-111857000	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:111855800-111856200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr3:111855800-111856200	Enhancers	Left Ventricle	heart
48	chr3:111855800-111856400	Enhancers	Brain Anterior Caudate	brain
49	chr3:111855800-111856400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:111855800-111857000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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