Variant report

Variant	rs2371455
Chromosome Location	chr12:56843893-56843894
allele	G/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	NRF1	chr12:56842544-56844018	SK-N-SH	brain:	n/a	chr12:56842948-56842957 chr12:56842946-56842957 chr12:56842971-56842980 chr12:56842943-56842957 chr12:56842946-56842960 chr12:56843187-56843196 chr12:56842946-56842957 chr12:56843190-56843199
2	POLR2A	chr12:56841144-56843990	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56842400-56844246	SK-N-MC	brain:	n/a	n/a
4	SIX5	chr12:56842353-56844015	A549	lung:	n/a	n/a
5	MXI1	chr12:56842301-56844522	SK-N-SH	brain:	n/a	chr12:56843229-56843238

No.	Distal block	Cell Line	Cell type
1	chr12:56841852..56845371-chr12:56847401..56851228,5	MCF-7	breast:
2	chr12:56751886..56753976-chr12:56841675..56844416,2	MCF-7	breast:
3	chr12:56660541..56662751-chr12:56842837..56845595,2	MCF-7	breast:
4	chr12:56823780..56826763-chr12:56843201..56845054,2	MCF-7	breast:
5	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
6	chr12:56843620..56845384-chr12:56856512..56859341,2	MCF-7	breast:
7	chr12:56684593..56687796-chr12:56843466..56846385,3	K562	blood:
8	chr12:56841673..56844476-chr12:56882161..56884243,2	MCF-7	breast:
9	chr12:56841526..56846188-chr12:56861608..56864760,4	K562	blood:
10	chr12:56510141..56512052-chr12:56841744..56844555,2	MCF-7	breast:
11	chr12:56726610..56729385-chr12:56842009..56844680,3	MCF-7	breast:
12	chr12:56726826..56730263-chr12:56843766..56846381,3	K562	blood:
13	chr12:56693766..56695727-chr12:56841370..56844312,2	K562	blood:
14	chr12:56753916..56755760-chr12:56841528..56845904,3	K562	blood:

Variant related genes	Relation type
TIMELESS	TF binding region
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10876889	0.84[ASN][1000 genomes]
rs10876890	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11171847	0.88[ASN][1000 genomes]
rs11171848	0.89[ASN][1000 genomes]
rs11171849	0.89[ASN][1000 genomes]
rs11171850	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs11171852	0.89[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11171856	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11610921	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11833581	0.86[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs11833583	0.89[ASN][1000 genomes]
rs12299614	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs12313431	0.89[ASN][1000 genomes]
rs12316810	0.93[ASN][1000 genomes]
rs12815993	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1976294	0.82[ASN][1000 genomes]
rs2279665	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2291738	0.89[CEU][hapmap]
rs2291739	0.82[ASW][hapmap]
rs2638304	0.86[ASN][1000 genomes]
rs2657882	0.85[ASN][1000 genomes]
rs2657883	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2939303	0.92[ASN][1000 genomes]
rs34520497	0.88[ASN][1000 genomes]
rs34644700	0.89[ASN][1000 genomes]
rs35634983	0.85[ASN][1000 genomes]
rs3782237	0.88[ASN][1000 genomes]
rs3809125	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581094	0.88[ASN][1000 genomes]
rs6581095	0.88[ASN][1000 genomes]
rs67027355	0.88[ASN][1000 genomes]
rs703829	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs7312888	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs774026	0.88[ASN][1000 genomes]
rs774027	0.82[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs774031	0.88[ASN][1000 genomes]
rs774032	0.88[ASN][1000 genomes]
rs774033	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs774034	0.85[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs774035	0.82[CEU][hapmap];0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs774036	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs774037	0.88[ASN][1000 genomes]
rs774039	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs774047	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs7977477	0.82[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs812278	0.82[ASN][1000 genomes]
rs812279	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2371455	TAC3	cis	parietal	SCAN
rs2371455	AMHR2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56842400-56844000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:56842400-56844000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr12:56842400-56844000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:56843200-56844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:56843400-56844000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:56843400-56844000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:56843400-56844200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:56843600-56844000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:56843600-56844000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:56843600-56844000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:56843600-56844000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:56843600-56844000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:56843600-56844200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:56843600-56844200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:56843600-56844200	Enhancers	Thymus	Thymus
16	chr12:56843600-56844600	Enhancers	HSMMtube	muscle
17	chr12:56843600-56844800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:56843600-56845200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:56843600-56845400	Enhancers	Fetal Thymus	thymus
20	chr12:56843600-56852800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:56843800-56844000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:56843800-56844000	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:56843800-56844000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:56843800-56844000	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr12:56843800-56844000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:56843800-56844000	Enhancers	Brain Substantia Nigra	brain
27	chr12:56843800-56844000	Enhancers	Colon Smooth Muscle	Colon
28	chr12:56843800-56844000	Enhancers	Fetal Heart	heart
29	chr12:56843800-56844000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr12:56843800-56844000	Enhancers	A549	lung
31	chr12:56843800-56844000	Enhancers	Hela-S3	cervix
32	chr12:56843800-56844000	Enhancers	HUVEC	blood vessel
33	chr12:56843800-56844200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:56843800-56844200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:56843800-56844200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:56843800-56844200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:56843800-56844200	Enhancers	Dnd41	blood
38	chr12:56843800-56844400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:56843800-56844400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:56843800-56844600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:56843800-56844600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:56843800-56844600	Enhancers	Fetal Muscle Leg	muscle
43	chr12:56843800-56844600	Enhancers	HepG2	liver
44	chr12:56843800-56844800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr12:56843800-56844800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr12:56843800-56844800	Enhancers	Primary T cells from cord blood	blood
47	chr12:56843800-56844800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr12:56843800-56845000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr12:56843800-56845000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:56843800-56845200	Enhancers	HUES48 Cell Line	embryonic stem cell

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