Variant report

Variant	rs4944949
Chromosome Location	chr11:71160395-71160396
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	MYC	chr11:71158283-71160560	NB4	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
2	MXI1	chr11:71159306-71160648	K562	blood:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
3	MXI1	chr11:71159325-71160501	Hela-S3	cervix:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
4	MAX	chr11:71158768-71160515	HCT-116	colon:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
5	MAX	chr11:71158858-71160597	Hela-S3	cervix:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
6	SIN3AK20	chr11:71157693-71160571	MCF-7	breast:	n/a	n/a
7	MAX	chr11:71158673-71160541	A549	lung:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
8	E2F6	chr11:71158890-71160400	A549	lung:	n/a	chr11:71159527-71159536 chr11:71159563-71159572 chr11:71159152-71159161 chr11:71159972-71159979 chr11:71159451-71159460
9	SIN3A	chr11:71158432-71160629	H1-hESC	embryonic stem cell:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71158949-71158962
10	NR2F2	chr11:71159680-71160926	K562	blood:	n/a	n/a
11	MYC	chr11:71158869-71161077	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
12	MAX	chr11:71158845-71160423	HCT-116	colon:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
13	MXI1	chr11:71158050-71161114	IMR90	lung:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
14	ZBTB7A	chr11:71158882-71160409	ECC-1	luminal epithelium:	n/a	chr11:71159649-71159660
15	POLR2A	chr11:71158416-71160416	Hela-S3	cervix:	n/a	n/a
16	MAX	chr11:71158743-71160539	HepG2	liver:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
17	BRCA1	chr11:71159358-71160464	Hela-S3	cervix:	n/a	n/a
18	GATA2	chr11:71160354-71160799	SH-SY5Y	brain:	n/a	n/a
19	MYC	chr11:71158882-71161096	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
20	MAX	chr11:71158866-71160577	Hela-S3	cervix:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
21	JUN	chr11:71159075-71160800	K562	blood:	n/a	chr11:71159482-71159491 chr11:71159426-71159436 chr11:71159153-71159162 chr11:71159426-71159436
22	MAX	chr11:71158207-71160474	NB4	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
23	MYC	chr11:71158869-71160915	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
24	MAX	chr11:71158263-71160426	HepG2	liver:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
25	HCFC1	chr11:71158357-71160850	Hela-S3	cervix:	n/a	n/a
26	MAX	chr11:71158640-71160437	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
27	GATA3	chr11:71160355-71160718	SH-SY5Y	brain:	n/a	n/a
28	MAX	chr11:71158618-71160479	MCF-7	breast:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
29	MXI1	chr11:71158250-71161741	SK-N-SH	brain:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
30	MYC	chr11:71159276-71160518	MCF10A-Er-Src	breast:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
31	MAX	chr11:71158712-71160405	ECC-1	luminal epithelium:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
32	MAX	chr11:71158356-71160499	MCF-7	breast:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
33	MAX	chr11:71159187-71160458	A549	lung:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
34	NR2F2	chr11:71159054-71160414	MCF-7	breast:	n/a	n/a
35	MAZ	chr11:71158254-71160633	IMR90	lung:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730

No.	Distal block	Cell Line	Cell type
1	chr11:71158745..71161047-chr14:24656517..24659263,2	MCF-7	breast:
2	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
3	chr11:70805722..70807297-chr11:71158455..71160766,2	MCF-7	breast:
4	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
5	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:

Variant related genes	Relation type
NADSYN1	TF binding region
DHCR7	TF binding region
ENSG00000204572	Chromatin interaction
ENSG00000162105	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1044482	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11233746	0.92[ASN][1000 genomes]
rs11233747	0.92[ASN][1000 genomes]
rs11546509	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11600569	0.92[ASN][1000 genomes]
rs11600860	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603330	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11604642	0.87[ASN][1000 genomes]
rs11606033	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11606612	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11606631	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419279	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12419334	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12422045	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12785878	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12789253	0.81[ASN][1000 genomes]
rs12789751	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12790010	0.92[ASN][1000 genomes]
rs12790558	0.92[ASN][1000 genomes]
rs12791871	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12792306	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12793224	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12793530	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12793607	0.81[ASN][1000 genomes]
rs12794668	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12797951	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12800438	0.92[ASN][1000 genomes]
rs12803256	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12806844	0.92[ASN][1000 genomes]
rs12807718	0.92[ASN][1000 genomes]
rs12807827	0.83[ASN][1000 genomes]
rs12808368	0.92[ASN][1000 genomes]
rs1981412	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2002063	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2040323	0.92[ASN][1000 genomes]
rs2276360	0.93[ASN][1000 genomes]
rs2276361	0.93[ASN][1000 genomes]
rs2276362	0.92[ASN][1000 genomes]
rs28364617	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852853	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3750997	0.81[ASN][1000 genomes]
rs3763856	0.81[ASN][1000 genomes]
rs3794060	0.92[ASN][1000 genomes]
rs4423214	0.92[ASN][1000 genomes]
rs4488226	0.93[ASN][1000 genomes]
rs4944062	0.92[ASN][1000 genomes]
rs4944946	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944955	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944956	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944958	0.93[ASN][1000 genomes]
rs4944959	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944996	0.94[ASN][1000 genomes]
rs4945008	0.87[ASN][1000 genomes]
rs732934	0.92[ASN][1000 genomes]
rs7928249	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7935125	0.92[ASN][1000 genomes]
rs7938885	0.92[ASN][1000 genomes]
rs7944926	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs909217	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4944949	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs4944949	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs4944949	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs4944949	NADSYN1	cis	Thyroid	GTEx
rs4944949	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs4944949	RP11-660L16.2	cis	Thyroid	GTEx
rs4944949	RP11-660L16.2	cis	Whole Blood	GTEx
rs4944949	DHCR7	cis	intralobular white matter	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71158000-71161000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:71158000-71161000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:71158400-71160400	Active TSS	HSMM	muscle
4	chr11:71158400-71160600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:71158400-71160600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr11:71158400-71160800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr11:71158400-71160800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:71158400-71160800	Active TSS	Rectal Smooth Muscle	rectum
9	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:71158400-71161400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:71158600-71160400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr11:71158600-71160400	Active TSS	Gastric	stomach
14	chr11:71158600-71160400	Active TSS	A549	lung
15	chr11:71158600-71160600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr11:71158600-71160800	Active TSS	Fetal Kidney	kidney
17	chr11:71158600-71160800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr11:71158600-71160800	Active TSS	Lung	lung
19	chr11:71158600-71160800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr11:71158600-71160800	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr11:71158600-71161000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:71158600-71161000	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr11:71158600-71161200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr11:71158600-71161200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr11:71158600-71161200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr11:71158600-71161200	Active TSS	HMEC	breast
27	chr11:71158600-71161400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr11:71158800-71160400	Active TSS	Small Intestine	intestine
29	chr11:71158800-71160600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:71158800-71160600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:71158800-71160600	Active TSS	Fetal Brain Male	brain
32	chr11:71158800-71160600	Active TSS	Ovary	ovary
33	chr11:71158800-71160600	Active TSS	Right Ventricle	heart
34	chr11:71158800-71160600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr11:71158800-71160800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:71158800-71160800	Active TSS	K562	blood
37	chr11:71158800-71161000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:71158800-71161000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr11:71158800-71161200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:71158800-71162000	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr11:71158800-71162000	Active TSS	GM12878-XiMat	blood
42	chr11:71159000-71160400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:71159000-71160400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:71159000-71160400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:71159000-71160400	Active TSS	Brain Substantia Nigra	brain
46	chr11:71159000-71160400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr11:71159000-71160400	Active TSS	Fetal Intestine Small	intestine
48	chr11:71159000-71160400	Active TSS	Osteobl	bone
49	chr11:71159000-71160600	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr11:71159000-71160600	Active TSS	Primary T killer memory cells from peripheral blood	blood

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