Variant report

Variant	rs2605380
Chromosome Location	chr12:74933166-74933167
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	POLR2A	chr12:74931200-74936073	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:74931151-74933337	GM18505	blood:	n/a	n/a
3	CHD1	chr12:74930901-74933411	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:74932890-74933398	GM12878	blood:	n/a	n/a
5	HA-E2F1	chr12:74931278-74933877	MCF-7	breast:	n/a	chr12:74931774-74931784 chr12:74931773-74931782 chr12:74931642-74931649 chr12:74931547-74931556
6	MXI1	chr12:74930680-74934315	SK-N-SH	brain:	n/a	chr12:74932789-74932798
7	TCF7L2	chr12:74931076-74933168	Hela-S3	cervix:	n/a	chr12:74932622-74932638
8	RCOR1	chr12:74932973-74933321	K562	blood:	n/a	n/a
9	POLR2A	chr12:74932960-74933202	MCF-7	breast:	n/a	n/a
10	USF2	chr12:74931898-74933602	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:74933005-74933263	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:74931110-74940575	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr12:74931116-74935658	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr12:74933049-74933230	ProgFib	skin:	n/a	n/a
15	POLR2A	chr12:74931201-74935166	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:74931286-74933257	GM19193	blood:	n/a	n/a
17	MAX	chr12:74932282-74933248	K562	blood:	n/a	chr12:74932790-74932800 chr12:74932789-74932800 chr12:74932790-74932799 chr12:74932788-74932801 chr12:74932790-74932800 chr12:74932788-74932801 chr12:74932786-74932801 chr12:74932789-74932800 chr12:74932791-74932800 chr12:74932792-74932799 chr12:74932789-74932800 chr12:74932789-74932798 chr12:74932788-74932801
18	WRNIP1	chr12:74931153-74935222	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr12:74931088-74933432	MCF-7	breast:	n/a	n/a
20	POLR2A	chr12:74933008-74933359	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:74933074-74933208	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:74931269-74934114	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:74932372-74934585	K562	blood:	n/a	n/a
24	BHLHE40	chr12:74932830-74933278	K562	blood:	n/a	n/a
25	POLR2A	chr12:74931307-74933432	Hela-S3	cervix:	n/a	n/a
26	BACH1	chr12:74933155-74933351	K562	blood:	n/a	n/a
27	POLR2A	chr12:74931142-74933843	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:74931195-74933842	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:74931126-74935588	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:74932912-74937655	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr12:74931025-74933502	PBDE	blood:	n/a	n/a
32	POLR2A	chr12:74932834-74933288	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:74931035-74936789	IMR90	lung:	n/a	n/a
34	POLR2A	chr12:74932414-74936105	A549	lung:	n/a	n/a
35	TBL1XR1	chr12:74932436-74933182	K562	blood:	n/a	n/a
36	POLR2A	chr12:74931091-74937173	GM12891	blood:	n/a	n/a
37	POLR2A	chr12:74931368-74933966	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:74686465..74688529-chr12:74932040..74934610,2	K562	blood:

Variant related genes	Relation type
ENSG00000257386	TF binding region
ENSG00000251138	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1037887	1.00[AFR][1000 genomes]
rs1389486	0.83[AFR][1000 genomes]
rs1389487	0.83[AFR][1000 genomes]
rs1389489	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1389490	1.00[AFR][1000 genomes]
rs1389491	1.00[AFR][1000 genomes]
rs1493798	1.00[AFR][1000 genomes]
rs1493804	1.00[AFR][1000 genomes]
rs1493807	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1563930	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1870699	1.00[AFR][1000 genomes]
rs1873987	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1873988	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2007674	1.00[AFR][1000 genomes]
rs2029717	1.00[AFR][1000 genomes]
rs2219608	1.00[AFR][1000 genomes]
rs2249335	0.83[AFR][1000 genomes]
rs2252250	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2605360	1.00[AFR][1000 genomes]
rs2605379	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613880	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613892	1.00[AFR][1000 genomes]
rs2613896	1.00[AFR][1000 genomes]
rs2613899	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2641465	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2925223	1.00[AFR][1000 genomes]
rs2925224	1.00[AFR][1000 genomes]
rs2926807	1.00[AFR][1000 genomes]
rs588875	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs590166	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs596999	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs625531	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs663854	1.00[AFR][1000 genomes]
rs694314	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs822806	1.00[YRI][hapmap]
rs822809	1.00[YRI][hapmap]
rs922222	0.83[AFR][1000 genomes]
rs970236	1.00[AFR][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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899292	chr12:74835107-74934162	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
6	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74931200-74934000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:74931800-74933600	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:74931800-74934000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
4	chr12:74932000-74933600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr12:74932000-74934000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:74932000-74934400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:74932000-74934400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:74932000-74935000	Transcr. at gene 5' and 3'	Fetal Lung	lung
9	chr12:74932200-74933600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr12:74932200-74933800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr12:74932200-74934000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:74932200-74934000	Flanking Active TSS	NH-A	brain
13	chr12:74932200-74934800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr12:74932200-74935200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr12:74932400-74933200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr12:74932400-74933200	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr12:74932400-74933200	Flanking Active TSS	Placenta	Placenta
18	chr12:74932400-74933400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:74932400-74933400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:74932400-74933400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:74932400-74933400	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr12:74932400-74933400	Flanking Active TSS	Right Atrium	heart
23	chr12:74932400-74933400	Flanking Active TSS	Right Ventricle	heart
24	chr12:74932400-74933600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:74932400-74933800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr12:74932400-74933800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:74932400-74933800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:74932400-74933800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:74932400-74933800	Flanking Active TSS	Fetal Thymus	thymus
30	chr12:74932400-74933800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:74932400-74933800	Flanking Active TSS	HMEC	breast
32	chr12:74932400-74933800	Flanking Active TSS	HSMMtube	muscle
33	chr12:74932400-74934000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:74932400-74934000	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr12:74932400-74934200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:74932400-74934200	Flanking Active TSS	Liver	Liver
37	chr12:74932400-74934200	Flanking Active TSS	Fetal Brain Male	brain
38	chr12:74932400-74934200	Flanking Active TSS	HUVEC	blood vessel
39	chr12:74932400-74934200	Transcr. at gene 5' and 3'	NHLF	lung
40	chr12:74932400-74934400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
41	chr12:74932400-74934600	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr12:74932400-74934800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:74932400-74934800	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr12:74932400-74934800	Flanking Active TSS	Thymus	Thymus
45	chr12:74932400-74935000	Transcr. at gene 5' and 3'	A549	lung
46	chr12:74932400-74935200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:74932400-74935200	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr12:74932400-74935400	Transcr. at gene 5' and 3'	NHEK	skin
49	chr12:74932600-74933200	Transcr. at gene 5' and 3'	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:74932600-74933200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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