Variant report

Variant	rs4749959
Chromosome Location	chr10:6128314-6128315
allele	C/T
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	REST	chr10:6128288-6128640	SK-N-SH	brain:	n/a	n/a
2	EP300	chr10:6128263-6128613	SK-N-SH_RA	brain:	n/a	chr10:6128289-6128303 chr10:6128525-6128535
3	REST	chr10:6128307-6128653	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr10:6128313-6128880	HCT-116	colon:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
5	YY1	chr10:6128217-6128732	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr10:6128125-6129074	A549	lung:	n/a	chr10:6128956-6128964 chr10:6128536-6128554 chr10:6128539-6128552
7	TEAD4	chr10:6128247-6128704	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXA2	chr10:6128312-6128684	HepG2	liver:	n/a	n/a
9	SIN3A	chr10:6128311-6128716	H1-hESC	embryonic stem cell:	n/a	chr10:6128464-6128473
10	CTCF	chr10:6128311-6128805	IMR90	lung:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
11	MAX	chr10:6128307-6128746	K562	blood:	n/a	n/a
12	CTCF	chr10:6128260-6128882	MCF-7	breast:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
13	EP300	chr10:6128269-6128708	H1-hESC	embryonic stem cell:	n/a	chr10:6128289-6128303 chr10:6128525-6128535
14	FOXP2	chr10:6128281-6128699	PFSK-1	brain:	n/a	n/a
15	CTCF	chr10:6128299-6128760	A549	lung:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
16	MAX	chr10:6128240-6128743	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOXM1	chr10:6128207-6128958	GM12878	blood:	n/a	n/a
18	ZNF384	chr10:6128125-6128826	K562	blood:	n/a	n/a
19	MTA3	chr10:6128236-6128810	GM12878	blood:	n/a	n/a
20	PAX5	chr10:6128313-6128682	GM12878	blood:	n/a	n/a
21	ELF1	chr10:6128286-6128782	GM12878	blood:	n/a	chr10:6128293-6128304
22	CTCF	chr10:6128257-6128818	MCF-7	breast:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
23	GATA2	chr10:6128158-6128998	SH-SY5Y	brain:	n/a	chr10:6128932-6128945 chr10:6128376-6128388 chr10:6128291-6128301 chr10:6128378-6128385
24	POLR2A	chr10:6128287-6128583	SK-N-SH	brain:	n/a	n/a
25	SP1	chr10:6128228-6128697	A549	lung:	n/a	chr10:6128279-6128289
26	ZNF384	chr10:6128139-6128716	GM12878	blood:	n/a	n/a
27	BCLAF1	chr10:6128307-6128756	GM12878	blood:	n/a	n/a
28	USF1	chr10:6128286-6128642	H1-hESC	embryonic stem cell:	n/a	n/a
29	BCLAF1	chr10:6128283-6128808	GM12878	blood:	n/a	n/a
30	SP1	chr10:6128290-6128691	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr10:6128233-6128748	H1-hESC	embryonic stem cell:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
32	TCF12	chr10:6128202-6128739	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr10:6128314-6128779	T-47D	breast:	n/a	chr10:6128536-6128554 chr10:6128539-6128552
34	CBX3	chr10:6128215-6128852	HCT-116	colon:	n/a	n/a
35	MAZ	chr10:6128296-6129088	K562	blood:	n/a	n/a
36	MAX	chr10:6128205-6128861	A549	lung:	n/a	n/a
37	TCF12	chr10:6128116-6128916	A549	lung:	n/a	n/a
38	BHLHE40	chr10:6128279-6128733	K562	blood:	n/a	n/a
39	FOXA1	chr10:6128288-6128702	HepG2	liver:	n/a	chr10:6128520-6128535
40	YY1	chr10:6128284-6128629	GM12892	blood:	n/a	n/a
41	EBF1	chr10:6128274-6128608	GM12878	blood:	n/a	n/a
42	FOXA2	chr10:6128273-6128699	A549	lung:	n/a	n/a
43	MYC	chr10:6128122-6128627	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr10:6128242-6128849	A549	lung:	n/a	chr10:6128535-6128548 chr10:6128432-6128451
45	NRF1	chr10:6128268-6128636	GM12878	blood:	n/a	n/a
46	TCF12	chr10:6128150-6128819	SK-N-SH	brain:	n/a	n/a
47	EP300	chr10:6128309-6128702	SK-N-SH_RA	brain:	n/a	chr10:6128525-6128535
48	TCF3	chr10:6128307-6128655	GM12878	blood:	n/a	n/a
49	CREB1	chr10:6128295-6128676	A549	lung:	n/a	n/a
50	TEAD4	chr10:6128268-6128782	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6121462..6124119-chr10:6127226..6129947,2	MCF-7	breast:
2	chr10:5991379..5992087-chr10:6128226..6129003,2	MCF-7	breast:
3	chr10:6128311..6129288-chr10:6448316..6448932,2	MCF-7	breast:
4	chr10:6055791..6056406-chr10:6128063..6128908,2	MCF-7	breast:

Variant related genes	Relation type
RBM17	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10905806	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3930531	0.84[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs4749957	0.83[EUR][1000 genomes]
rs7911362	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv894815	chr10:6108439-6161781	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6124800-6131000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:6126000-6128600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr10:6126000-6130400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr10:6126000-6131000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:6126200-6131000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:6127200-6129200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr10:6127800-6129200	Enhancers	Primary B cells from peripheral blood	blood
8	chr10:6128000-6128400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr10:6128000-6128600	Enhancers	Fetal Muscle Trunk	muscle
10	chr10:6128000-6129000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:6128200-6128400	Enhancers	Primary hematopoietic stem cells	blood
12	chr10:6128200-6128400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr10:6128200-6128400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:6128200-6128400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr10:6128200-6128400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:6128200-6128400	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr10:6128200-6128400	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr10:6128200-6128400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr10:6128200-6128400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:6128200-6128400	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr10:6128200-6128400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr10:6128200-6128400	Enhancers	Esophagus	oesophagus
23	chr10:6128200-6128400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr10:6128200-6128400	Flanking Active TSS	Placenta	Placenta
25	chr10:6128200-6128400	Flanking Active TSS	Psoas Muscle	Psoas
26	chr10:6128200-6128400	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr10:6128200-6128400	Enhancers	Right Atrium	heart
28	chr10:6128200-6128400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr10:6128200-6128400	Enhancers	Small Intestine	intestine
30	chr10:6128200-6128400	Flanking Active TSS	HSMM	muscle
31	chr10:6128200-6128400	Flanking Active TSS	HSMMtube	muscle
32	chr10:6128200-6128400	Flanking Active TSS	HUVEC	blood vessel
33	chr10:6128200-6128400	Enhancers	NH-A	brain
34	chr10:6128200-6128400	Flanking Active TSS	NHDF-Ad	bronchial
35	chr10:6128200-6128400	Active TSS	NHLF	lung
36	chr10:6128200-6128600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:6128200-6128600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:6128200-6128600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:6128200-6128600	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr10:6128200-6128600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr10:6128200-6128600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr10:6128200-6128600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:6128200-6128600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr10:6128200-6128600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:6128200-6128600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:6128200-6128600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:6128200-6128600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr10:6128200-6128600	Enhancers	Aorta	Aorta
49	chr10:6128200-6128600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr10:6128200-6128600	Active TSS	Fetal Kidney	kidney

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