Variant report

Variant	rs3755636
Chromosome Location	chr3:135968828-135968829
allele	C/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	MXI1	chr3:135968554-135970729	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:135968640-135970593	GM12878	blood:	n/a	n/a
3	MYC	chr3:135968702-135970404	K562	blood:	n/a	chr3:135969975-135969985
4	NFIC	chr3:135968698-135970035	HepG2	liver:	n/a	n/a
5	RUNX3	chr3:135968822-135970578	GM12878	blood:	n/a	n/a
6	GTF3C2	chr3:135968625-135969440	K562	blood:	n/a	n/a
7	MAFF	chr3:135968799-135969678	HepG2	liver:	n/a	chr3:135969202-135969220
8	HCFC1	chr3:135968361-135970554	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:135968497-135970273	Raji	blood:	n/a	n/a
10	MTA3	chr3:135968669-135969505	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:135968738-135969625	GM10847	blood:	n/a	n/a
12	POLR2A	chr3:135968798-135970334	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr3:135968768-135969758	GM12878	blood:	n/a	n/a
14	ZNF384	chr3:135968303-135969389	K562	blood:	n/a	n/a
15	POLR2A	chr3:135968821-135969675	U87	brain:	n/a	n/a
16	TBL1XR1	chr3:135968774-135969989	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:135968573-135970337	GM15510	blood:	n/a	n/a
18	POLR2A	chr3:135968757-135970751	SK-N-MC	brain:	n/a	n/a
19	MAX	chr3:135968770-135970462	HepG2	liver:	n/a	chr3:135969975-135969985
20	MAX	chr3:135968757-135970325	ECC-1	luminal epithelium:	n/a	chr3:135969975-135969985
21	NFIC	chr3:135968698-135969210	GM12878	blood:	n/a	n/a
22	HEY1	chr3:135968804-135969826	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:135968802-135969786	PFSK-1	brain:	n/a	n/a
24	YY1	chr3:135968803-135969822	SK-N-SH	brain:	n/a	n/a
25	MYBL2	chr3:135968721-135970274	HepG2	liver:	n/a	n/a
26	PML	chr3:135968621-135970374	GM12878	blood:	n/a	n/a
27	NRF1	chr3:135968783-135969777	SK-N-SH	brain:	n/a	chr3:135969142-135969153 chr3:135969139-135969153 chr3:135969142-135969151 chr3:135969167-135969178 chr3:135969141-135969152
28	STAT5A	chr3:135968803-135969537	GM12878	blood:	n/a	n/a
29	MYC	chr3:135968735-135970581	A549	lung:	n/a	chr3:135969975-135969985
30	CTCF	chr3:135968622-135969663	A549	lung:	n/a	chr3:135969505-135969518 chr3:135969187-135969203
31	BCLAF1	chr3:135968732-135969383	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:135968704-135970253	GM19099	blood:	n/a	n/a
33	MAZ	chr3:135968762-135970507	GM12878	blood:	n/a	n/a
34	GTF3C2	chr3:135968669-135969254	Hela-S3	cervix:	n/a	n/a
35	ATF2	chr3:135968769-135969758	GM12878	blood:	n/a	n/a
36	CEBPB	chr3:135968446-135969485	HepG2	liver:	n/a	chr3:135968595-135968606
37	POLR2A	chr3:135968826-135969783	HCT-116	colon:	n/a	n/a
38	SIN3AK20	chr3:135968725-135970082	MCF-7	breast:	n/a	n/a
39	POLR2A	chr3:135968584-135970344	GM12892	blood:	n/a	n/a
40	POLR2A	chr3:135968775-135970420	K562	blood:	n/a	n/a
41	MAX	chr3:135968771-135970378	ECC-1	luminal epithelium:	n/a	chr3:135969975-135969985
42	STAT3	chr3:135968820-135969103	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr3:135968798-135970641	K562	blood:	n/a	chr3:135969975-135969985
44	REST	chr3:135968698-135969860	H1-neurons	neurons:	n/a	chr3:135969050-135969063 chr3:135969047-135969060
45	CEBPB	chr3:135968445-135969893	Hela-S3	cervix:	n/a	chr3:135968595-135968606
46	CREB1	chr3:135968521-135970339	HepG2	liver:	n/a	n/a
47	SMARCB1	chr3:135968566-135969599	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr3:135968818-135970105	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr3:135968635-135970628	GM12891	blood:	n/a	n/a
50	STAT1	chr3:135968749-135969491	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:135968568..135972532-chr3:135974380..135977728,5	K562	blood:
2	chr3:135967895..135971293-chr3:135973278..135977937,5	MCF-7	breast:
3	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
4	chr3:135968756..135970580-chr3:136469634..136471998,2	K562	blood:
5	chr3:135968107..135969967-chr3:136470513..136472370,2	MCF-7	breast:
6	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:
7	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
8	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
9	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:

Variant related genes	Relation type
PCCB	TF binding region
ENSG00000118007	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10935177	0.86[JPT][hapmap]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs1145106	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1153870	0.85[ASN][1000 genomes]
rs1153871	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153872	0.87[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.83[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs11717954	0.87[JPT][hapmap]
rs12330635	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs1278493	0.86[JPT][hapmap]
rs1278719	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs1279425	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1279840	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1291921	0.86[ASN][1000 genomes]
rs1618069	0.87[ASN][1000 genomes]
rs1711161	0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs1711170	0.86[JPT][hapmap]
rs1711171	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17252498	0.82[CEU][hapmap]
rs2655008	0.93[JPT][hapmap]
rs3772390	0.88[CHB][hapmap]
rs3821445	0.88[CEU][hapmap]
rs3957816	0.86[JPT][hapmap]
rs4678428	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483465	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs523118	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs534944	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs548288	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs576771	0.84[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61789601	0.80[EUR][1000 genomes]
rs619605	0.93[JPT][hapmap]
rs632016	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439638	0.85[YRI][hapmap]
rs645040	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650326	1.00[JPT][hapmap]
rs650505	0.91[ASN][1000 genomes]
rs654237	0.93[JPT][hapmap]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs665200	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs667920	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6770476	0.80[ASN][1000 genomes]
rs6776841	0.81[YRI][hapmap]
rs6783337	0.80[YRI][hapmap]
rs6791611	0.87[JPT][hapmap]
rs684773	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs687339	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695983	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs696081	1.00[JPT][hapmap]
rs696516	0.93[JPT][hapmap]
rs696517	0.88[CEU][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs72493178	0.93[ASN][1000 genomes]
rs73222262	0.92[ASN][1000 genomes]
rs7372313	0.86[JPT][hapmap]
rs7628146	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895893	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs895894	0.86[JPT][hapmap]
rs9826146	0.87[YRI][hapmap]
rs9831321	0.89[YRI][hapmap]
rs9832056	0.90[CHB][hapmap]
rs9832813	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs9833162	0.81[YRI][hapmap]
rs9840812	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs9843801	0.87[YRI][hapmap]
rs9845457	0.86[JPT][hapmap]
rs9848883	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9851986	0.89[CHB][hapmap]
rs9853387	0.82[YRI][hapmap]
rs9856769	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9860801	0.82[YRI][hapmap]
rs9868120	0.89[YRI][hapmap]
rs9869720	0.89[CHB][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135967600-135969000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:135968000-135969000	Flanking Active TSS	HepG2	liver
3	chr3:135968600-135969000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:135968600-135969000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:135968600-135969000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:135968600-135969000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:135968600-135969000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:135968600-135969000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr3:135968600-135969000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:135968600-135969000	Flanking Active TSS	Liver	Liver
11	chr3:135968600-135969000	Flanking Active TSS	Brain Substantia Nigra	brain
12	chr3:135968600-135969000	Flanking Active TSS	GM12878-XiMat	blood
13	chr3:135968600-135969000	Flanking Active TSS	Hela-S3	cervix
14	chr3:135968600-135969000	Flanking Active TSS	NHEK	skin
15	chr3:135968600-135969000	Flanking Active TSS	Osteobl	bone
16	chr3:135968600-135969200	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr3:135968600-135969200	Flanking Active TSS	Dnd41	blood
18	chr3:135968600-135969400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:135968600-135969600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:135968600-135969600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:135968600-135969600	Active TSS	Brain Germinal Matrix	brain
22	chr3:135968600-135969600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:135968600-135969800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:135968600-135969800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:135968600-135969800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:135968600-135969800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:135968600-135969800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:135968600-135969800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:135968600-135969800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:135968600-135969800	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr3:135968600-135969800	Active TSS	Brain Anterior Caudate	brain
32	chr3:135968600-135969800	Active TSS	Fetal Brain Female	brain
33	chr3:135968600-135969800	Active TSS	Fetal Intestine Large	intestine
34	chr3:135968600-135969800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr3:135968600-135969800	Enhancers	Spleen	Spleen
36	chr3:135968600-135970000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:135968600-135970200	Active TSS	Fetal Lung	lung
38	chr3:135968600-135970200	Active TSS	Rectal Smooth Muscle	rectum
39	chr3:135968600-135970400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr3:135968600-135970400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr3:135968800-135969000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
42	chr3:135968800-135969000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:135968800-135969000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:135968800-135969000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:135968800-135969000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:135968800-135969000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:135968800-135969000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr3:135968800-135969000	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr3:135968800-135969000	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr3:135968800-135969000	Flanking Active TSS	Primary hematopoietic stem cells	blood

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