Variant report

Variant	rs11749955
Chromosome Location	chr5:40834182-40834183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:127)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:127 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40833886-40836321	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:40824786-40836349	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:40833397-40836297	GM15510	blood:	n/a	n/a
4	POLR2A	chr5:40833540-40836475	HL-60	blood:	n/a	n/a
5	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
6	MYC	chr5:40833754-40836963	K562	blood:	n/a	n/a
7	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
8	CHD2	chr5:40834004-40836006	K562	blood:	n/a	n/a
9	POLR2A	chr5:40833813-40836384	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIX5	chr5:40834050-40834830	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
12	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
13	ZBTB33	chr5:40834094-40834424	K562	blood:	n/a	n/a
14	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
15	IRF1	chr5:40833040-40835975	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
16	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
17	SP1	chr5:40834068-40834930	H1-hESC	embryonic stem cell:	n/a	n/a
18	MXI1	chr5:40834033-40835793	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:40833859-40835989	GM12891	blood:	n/a	n/a
20	POLR2A	chr5:40833129-40836609	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:40833996-40836057	H1-hESC	embryonic stem cell:	n/a	n/a
22	PML	chr5:40833820-40836144	K562	blood:	n/a	chr5:40835321-40835329
23	WRNIP1	chr5:40833235-40836410	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:40834076-40834500	HepG2	liver:	n/a	n/a
25	STAT3	chr5:40834053-40834253	MCF10A-Er-Src	breast:	n/a	n/a
26	GATA3	chr5:40834103-40834861	T-47D	breast:	n/a	n/a
27	POLR2A	chr5:40833681-40836203	HUVEC	blood vessel:	n/a	n/a
28	IRF1	chr5:40834129-40836010	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
29	POLR2A	chr5:40832988-40835995	GM12892	blood:	n/a	n/a
30	POLR2A	chr5:40833376-40836533	Hela-S3	cervix:	n/a	n/a
31	USF2	chr5:40833426-40836685	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr5:40832742-40836593	PANC-1	pancreas:	n/a	n/a
33	GABPA	chr5:40834089-40836341	A549	lung:	n/a	n/a
34	POLR2A	chr5:40826353-40836595	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:40825968-40836481	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:40833851-40835849	HCT-116	colon:	n/a	n/a
37	HEY1	chr5:40834177-40834730	HepG2	liver:	n/a	n/a
38	SMARCB1	chr5:40833425-40836418	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:40824347-40836356	U87	brain:	n/a	n/a
40	MTA3	chr5:40834102-40836016	GM12878	blood:	n/a	n/a
41	RELA	chr5:40834089-40836053	GM18505	blood:	n/a	n/a
42	POLR2A	chr5:40833106-40836648	K562	blood:	n/a	n/a
43	POLR2A	chr5:40833943-40834192	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr5:40833006-40836182	MCF-7	breast:	n/a	n/a
45	EP300	chr5:40833659-40836504	K562	blood:	n/a	n/a
46	PML	chr5:40834070-40836022	GM12878	blood:	n/a	chr5:40835321-40835329
47	POLR2A	chr5:40824803-40836847	Hela-S3	cervix:	n/a	n/a
48	HEY1	chr5:40833081-40836488	K562	blood:	n/a	n/a
49	POLR2A	chr5:40833210-40836619	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr5:40833949-40835790	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
2	chr17:8198296..8199051-chr5:40833703..40834545,2	Hela-S3	cervix:
3	chr1:149900207..149902355-chr5:40832606..40834765,2	MCF-7	breast:
4	chr5:40762484..40765387-chr5:40833487..40838148,4	K562	blood:
5	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
6	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
7	chr5:40833991..40836420-chr5:41902681..41904929,3	K562	blood:
8	chr5:40833974..40834885-chr6:31508984..31509608,2	Hela-S3	cervix:
9	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
10	chr5:40789707..40791650-chr5:40833757..40835320,2	K562	blood:
11	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
12	chr1:149858456..149859986-chr5:40833944..40836674,2	MCF-7	breast:
13	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
14	chr12:48448475..48449474-chr5:40834158..40834864,2	Hela-S3	cervix:
15	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
16	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:

No data

Variant related genes	Relation type
RPL37	TF binding region
SNORD72	TF binding region
ENSG00000132356	Chromatin interaction
ENSG00000240399	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000125434	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000143368	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10064650	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1070444	0.85[AMR][1000 genomes]
rs11743132	1.00[ASN][1000 genomes]
rs11743196	1.00[ASN][1000 genomes]
rs11746535	1.00[ASN][1000 genomes]
rs11748087	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11748743	1.00[ASN][1000 genomes]
rs12186450	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62357568	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62357569	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62357570	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62357571	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62357574	0.94[AMR][1000 genomes]
rs62357600	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv518711	chr5:40827307-40835627	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	137 gene(s)	inside rSNPs	diseases
4	nsv968907	chr5:40832497-40834810	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11749955	CARD6	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40830200-40834800	Transcr. at gene 5' and 3'	Hela-S3	cervix
2	chr5:40831200-40834400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
3	chr5:40831400-40834600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:40831400-40835000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:40831600-40835000	Transcr. at gene 5' and 3'	K562	blood
6	chr5:40831800-40834800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr5:40831800-40835000	Transcr. at gene 5' and 3'	A549	lung
8	chr5:40831800-40835200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
9	chr5:40832000-40835000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
10	chr5:40832000-40835200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
11	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:40832200-40834600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
14	chr5:40832200-40834600	Transcr. at gene 5' and 3'	NH-A	brain
15	chr5:40832200-40835000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
16	chr5:40832200-40835000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr5:40832400-40834800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr5:40832600-40834400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:40832600-40834400	Transcr. at gene 5' and 3'	HepG2	liver
20	chr5:40832600-40834400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
21	chr5:40832600-40834600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
22	chr5:40832600-40834600	Transcr. at gene 5' and 3'	HMEC	breast
23	chr5:40832600-40834800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
24	chr5:40832600-40834800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
25	chr5:40832600-40834800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:40832600-40835200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
27	chr5:40832800-40834600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:40832800-40834600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:40832800-40834800	Transcr. at gene 5' and 3'	Osteobl	bone
30	chr5:40832800-40835000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:40832800-40835000	Transcr. at gene 5' and 3'	NHLF	lung
32	chr5:40833000-40834200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:40833000-40834200	Enhancers	Small Intestine	intestine
34	chr5:40833000-40834400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:40833000-40834400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
36	chr5:40833000-40835000	Transcr. at gene 5' and 3'	NHEK	skin
37	chr5:40833200-40834200	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:40833200-40834200	Strong transcription	Aorta	Aorta
42	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
43	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
44	chr5:40833200-40834200	Transcr. at gene 5' and 3'	Thymus	Thymus
45	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
46	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
49	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
50	chr5:40833200-40834400	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas

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