Variant report

Variant	rs508904
Chromosome Location	chr12:57882094-57882095
allele	A/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	HEY1	chr12:57881688-57882253	K562	blood:	n/a	n/a
2	USF1	chr12:57881536-57882097	ECC-1	luminal epithelium:	n/a	n/a
3	MYC	chr12:57881477-57882122	MCF-7	breast:	n/a	chr12:57881847-57881856
4	MAX	chr12:57881419-57882114	K562	blood:	n/a	chr12:57881847-57881856
5	POLR2A	chr12:57881645-57882137	GM12892	blood:	n/a	n/a
6	SIN3AK20	chr12:57881429-57882194	MCF-7	breast:	n/a	n/a
7	POLR2A	chr12:57881333-57882267	GM12892	blood:	n/a	n/a
8	NFATC1	chr12:57881496-57882143	GM12878	blood:	n/a	n/a
9	TCF12	chr12:57881276-57882206	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:57881445-57882142	Raji	blood:	n/a	n/a
11	ELF1	chr12:57881455-57882146	SK-N-SH	brain:	n/a	chr12:57881807-57881819
12	POLR2A	chr12:57881662-57882391	IMR90	lung:	n/a	n/a
13	POLR2A	chr12:57881611-57882173	Hela-S3	cervix:	n/a	n/a
14	ATF1	chr12:57881609-57882222	K562	blood:	n/a	n/a
15	POLR2A	chr12:57881637-57882115	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:57881693-57882123	GM12878	blood:	n/a	n/a
17	SIN3AK20	chr12:57881600-57882775	K562	blood:	n/a	n/a
18	SIN3AK20	chr12:57881586-57882138	PFSK-1	brain:	n/a	n/a
19	TAF7	chr12:57881597-57882158	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:57881399-57882621	U87	brain:	n/a	n/a
21	POLR2A	chr12:57881399-57882617	U87	brain:	n/a	n/a
22	SP1	chr12:57881359-57882140	A549	lung:	n/a	chr12:57882015-57882027 chr12:57882012-57882026 chr12:57882017-57882026 chr12:57882015-57882027 chr12:57882016-57882025
23	POLR2A	chr12:57881653-57882185	K562	blood:	n/a	n/a
24	SIN3AK20	chr12:57881527-57882255	A549	lung:	n/a	n/a
25	TAF1	chr12:57881329-57882541	ECC-1	luminal epithelium:	n/a	n/a
26	ELF1	chr12:57881443-57882166	MCF-7	breast:	n/a	chr12:57881807-57881819
27	GABPA	chr12:57881392-57882151	K562	blood:	n/a	n/a
28	SIX5	chr12:57881408-57882150	A549	lung:	n/a	chr12:57881783-57881797
29	MAX	chr12:57881401-57882278	A549	lung:	n/a	chr12:57881847-57881856
30	GABPA	chr12:57881437-57882223	HL-60	blood:	n/a	n/a
31	YY1	chr12:57881497-57882130	GM12892	blood:	n/a	chr12:57881782-57881799
32	CCNT2	chr12:57881627-57882140	K562	blood:	n/a	n/a
33	POLR2A	chr12:57881422-57882568	SK-N-MC	brain:	n/a	n/a
34	CREB1	chr12:57881574-57882123	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr12:57881667-57882175	GM18505	blood:	n/a	n/a
36	CEBPB	chr12:57881450-57882289	GM12878	blood:	n/a	chr12:57882056-57882067
37	POLR2A	chr12:57881403-57882687	K562	blood:	n/a	n/a
38	POLR2A	chr12:57881660-57882211	GM12878	blood:	n/a	n/a
39	JUND	chr12:57881552-57882116	H1-hESC	embryonic stem cell:	n/a	chr12:57882014-57882023 chr12:57882015-57882024
40	TBP	chr12:57881567-57882097	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr12:57881396-57882374	SK-N-SH	brain:	n/a	chr12:57881782-57881799
42	CEBPD	chr12:57881616-57882116	HepG2	liver:	n/a	chr12:57881845-57881856
43	ETS1	chr12:57881475-57882197	K562	blood:	n/a	chr12:57881783-57881796 chr12:57881839-57881848
44	POLR2A	chr12:57881379-57882721	GM12878	blood:	n/a	n/a
45	PAX5	chr12:57881386-57882181	GM12878	blood:	n/a	chr12:57882150-57882159 chr12:57882153-57882162
46	SPI1	chr12:57881624-57882262	GM12891	blood:	n/a	chr12:57882150-57882159
47	POLR2A	chr12:57881573-57882184	GM12891	blood:	n/a	n/a
48	YY1	chr12:57881451-57882154	GM12878	blood:	n/a	chr12:57881782-57881799
49	POLR2A	chr12:57881556-57882103	GM18951	blood:	n/a	n/a
50	POLR2A	chr12:57881684-57882118	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:
2	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
3	chr12:57866650..57869717-chr12:57880833..57883787,3	MCF-7	breast:
4	chr12:57880356..57884964-chr12:57910434..57915758,10	MCF-7	breast:
5	chr12:57881788..57882314-chr5:74806957..74807584,2	NB4	blood:
6	chr12:57881369..57883611-chr12:57902104..57905410,4	MCF-7	breast:
7	chr12:57880552..57883318-chr12:57915762..57917586,2	MCF-7	breast:
8	chr12:57880789..57883714-chr12:57919502..57921245,2	K562	blood:
9	chr12:57854130..57857750-chr12:57881459..57884101,5	K562	blood:
10	chr12:57855324..57857821-chr12:57881155..57883248,2	MCF-7	breast:
11	chr12:57881044..57886958-chr12:57910925..57918058,16	MCF-7	breast:
12	chr12:57824473..57826346-chr12:57880233..57882392,2	MCF-7	breast:
13	chr12:57881658..57883601-chr12:57939659..57941613,2	MCF-7	breast:
14	chr12:57869556..57871935-chr12:57881103..57884583,3	K562	blood:
15	chr12:57848182..57850484-chr12:57880307..57884604,3	K562	blood:
16	chr12:57881482..57885096-chr12:57938469..57941069,3	K562	blood:
17	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLI1-2	chr12:57881995-57882444	NONHSAT028924

Variant related genes	Relation type
MARS	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000252865	Chromatin interaction
ENSG00000113163	Chromatin interaction
ENSG00000122008	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000139269	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1148554	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1148555	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1284465	0.86[AMR][1000 genomes]
rs1284605	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1284606	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1299737	0.85[AMR][1000 genomes]
rs1617196	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1629410	0.85[AMR][1000 genomes]
rs1669296	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1678537	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1709871	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1709874	0.82[AMR][1000 genomes]
rs2620677	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2672571	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2673326	0.83[AMR][1000 genomes]
rs2943696	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs472895	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474544	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs496245	0.83[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs511752	0.83[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs539244	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs541869	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs542278	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs569251	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs697221	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs747340	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs776038	0.83[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs776039	0.82[AMR][1000 genomes]
rs796546	0.85[AMR][1000 genomes]
rs899653	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9737891	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv819781	chr12:57873564-57882217	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
15	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
16	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs508904	DCTN2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57881000-57882200	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:57881000-57882400	Active TSS	Colon Smooth Muscle	Colon
3	chr12:57881000-57882400	Active TSS	Fetal Lung	lung
4	chr12:57881000-57882800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:57881200-57882400	Active TSS	Fetal Intestine Small	intestine
6	chr12:57881200-57882400	Active TSS	Ovary	ovary
7	chr12:57881200-57882600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:57881200-57882600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:57881200-57882600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr12:57881200-57882600	Active TSS	Colonic Mucosa	Colon
11	chr12:57881200-57882600	Active TSS	Psoas Muscle	Psoas
12	chr12:57881200-57882600	Active TSS	Stomach Mucosa	stomach
13	chr12:57881200-57882800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:57881200-57882800	Active TSS	Muscle Satellite Cultured Cells	--
15	chr12:57881200-57882800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:57881200-57883000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:57881200-57883000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr12:57881200-57883400	Active TSS	Fetal Kidney	kidney
19	chr12:57881400-57882200	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr12:57881400-57882200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:57881400-57882200	Active TSS	Brain Germinal Matrix	brain
22	chr12:57881400-57882200	Active TSS	Fetal Brain Female	brain
23	chr12:57881400-57882200	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr12:57881400-57882200	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:57881400-57882400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:57881400-57882400	Active TSS	Brain Angular Gyrus	brain
27	chr12:57881400-57882400	Active TSS	Brain Anterior Caudate	brain
28	chr12:57881400-57882400	Active TSS	Brain Hippocampus Middle	brain
29	chr12:57881400-57882400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr12:57881400-57882400	Active TSS	Brain Substantia Nigra	brain
31	chr12:57881400-57882400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:57881400-57882400	Active TSS	Fetal Stomach	stomach
33	chr12:57881400-57882400	Active TSS	Thymus	Thymus
34	chr12:57881400-57882400	Active TSS	K562	blood
35	chr12:57881400-57882600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:57881400-57882600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr12:57881400-57882600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr12:57881400-57882600	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr12:57881400-57882600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:57881400-57882600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:57881400-57882600	Active TSS	Esophagus	oesophagus
42	chr12:57881400-57882600	Active TSS	Hela-S3	cervix
43	chr12:57881400-57882600	Active TSS	HSMM	muscle
44	chr12:57881400-57882600	Active TSS	NH-A	brain
45	chr12:57881400-57882600	Active TSS	NHEK	skin
46	chr12:57881400-57882600	Active TSS	Osteobl	bone
47	chr12:57881400-57882800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr12:57881400-57882800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr12:57881400-57882800	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr12:57881400-57882800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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