Variant report

Variant	rs1918496
Chromosome Location	chr12:56722060-56722061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56721940-56722283	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56691813..56695703-chr12:56721381..56724964,3	MCF-7	breast:
2	chr12:56719398..56723461-chr12:56725214..56730868,13	MCF-7	breast:
3	chr12:56721224..56722763-chr12:56723091..56725341,2	MCF-7	breast:
4	chr12:56720873..56724995-chr12:56726677..56728710,3	MCF-7	breast:
5	chr12:56707850..56716783-chr12:56721562..56730442,13	MCF-7	breast:
6	chr12:56719333..56720994-chr12:56721130..56724008,3	K562	blood:
7	chr12:56708838..56711187-chr12:56720390..56723412,3	MCF-7	breast:
8	chr12:56718035..56719704-chr12:56720082..56722862,2	MCF-7	breast:
9	chr12:56721052..56723021-chr12:56754281..56756582,2	MCF-7	breast:

No data

Variant related genes	Relation type
PAN2	TF binding region
ENSG00000135473	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000144785	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10876882	0.94[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10876885	1.00[EUR][1000 genomes]
rs1091527	1.00[EUR][1000 genomes]
rs11171812	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11171818	1.00[EUR][1000 genomes]
rs11171819	1.00[EUR][1000 genomes]
rs11171822	1.00[EUR][1000 genomes]
rs11575221	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575234	0.87[AFR][1000 genomes]
rs11575236	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11830379	1.00[EUR][1000 genomes]
rs11832580	1.00[EUR][1000 genomes]
rs11833064	1.00[EUR][1000 genomes]
rs11834948	1.00[EUR][1000 genomes]
rs11835018	1.00[EUR][1000 genomes]
rs11835310	1.00[EUR][1000 genomes]
rs12306512	1.00[EUR][1000 genomes]
rs12318887	1.00[EUR][1000 genomes]
rs12322356	1.00[EUR][1000 genomes]
rs1274493	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1626158	1.00[EUR][1000 genomes]
rs1689517	1.00[EUR][1000 genomes]
rs1689518	1.00[EUR][1000 genomes]
rs1702872	1.00[EUR][1000 genomes]
rs17118461	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17118590	1.00[EUR][1000 genomes]
rs2020854	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2066808	0.94[ASW][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2371494	0.94[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2629445	1.00[EUR][1000 genomes]
rs2629447	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2640566	1.00[EUR][1000 genomes]
rs2643623	0.89[AFR][1000 genomes]
rs2643626	0.89[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2661728	1.00[EUR][1000 genomes]
rs2661729	1.00[EUR][1000 genomes]
rs2695782	0.89[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2695788	0.87[AFR][1000 genomes]
rs2695789	0.89[ASW][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2934152	1.00[EUR][1000 genomes]
rs4301822	1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4417324	1.00[EUR][1000 genomes]
rs4996382	0.82[AMR][1000 genomes]
rs57237559	1.00[EUR][1000 genomes]
rs57387549	1.00[EUR][1000 genomes]
rs58349500	1.00[EUR][1000 genomes]
rs59286728	1.00[EUR][1000 genomes]
rs61733171	1.00[EUR][1000 genomes]
rs61733875	1.00[EUR][1000 genomes]
rs6581093	1.00[EUR][1000 genomes]
rs703830	0.94[AFR][1000 genomes]
rs72478990	1.00[EUR][1000 genomes]
rs7298109	1.00[EUR][1000 genomes]
rs7300292	1.00[EUR][1000 genomes]
rs7304690	1.00[EUR][1000 genomes]
rs7309327	1.00[EUR][1000 genomes]
rs73324336	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73324353	1.00[EUR][1000 genomes]
rs73324358	1.00[EUR][1000 genomes]
rs73338377	1.00[EUR][1000 genomes]
rs73338385	1.00[EUR][1000 genomes]
rs74094726	1.00[EUR][1000 genomes]
rs773652	0.89[ASW][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs773664	0.93[AFR][1000 genomes]
rs773665	0.89[ASW][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7954155	1.00[EUR][1000 genomes]
rs7954200	1.00[EUR][1000 genomes]
rs7962107	1.00[EUR][1000 genomes]
rs7975405	1.00[EUR][1000 genomes]
rs7977692	1.00[EUR][1000 genomes]
rs7979812	1.00[EUR][1000 genomes]
rs808919	0.95[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs901073	0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56710600-56726800	Weak transcription	NH-A	brain
2	chr12:56710800-56726400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:56710800-56726600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:56711000-56722400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:56711000-56722600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:56711000-56722800	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:56711200-56722400	Strong transcription	Fetal Stomach	stomach
8	chr12:56711400-56722600	Strong transcription	Liver	Liver
9	chr12:56711400-56726600	Weak transcription	Fetal Brain Male	brain
10	chr12:56711600-56722600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:56711600-56722800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:56711800-56722800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:56712000-56722400	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:56712000-56722600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:56712000-56722600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:56712000-56722800	Strong transcription	Fetal Intestine Large	intestine
17	chr12:56712000-56722800	Strong transcription	Placenta	Placenta
18	chr12:56712000-56724000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:56712200-56722400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:56712200-56722600	Strong transcription	Primary B cells from cord blood	blood
21	chr12:56712600-56722400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:56712600-56722600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:56712600-56722600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr12:56712600-56722600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:56712600-56722600	Strong transcription	Thymus	Thymus
26	chr12:56712800-56722400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:56712800-56722600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:56712800-56722600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:56712800-56722600	Strong transcription	Fetal Intestine Small	intestine
30	chr12:56713200-56722600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56713200-56722600	Strong transcription	Fetal Lung	lung
32	chr12:56713400-56726600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:56715000-56722400	Strong transcription	Brain Germinal Matrix	brain
34	chr12:56715000-56722600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:56715000-56722600	Strong transcription	Ovary	ovary
36	chr12:56715400-56722600	Strong transcription	Fetal Thymus	thymus
37	chr12:56715600-56722200	Strong transcription	Brain Hippocampus Middle	brain
38	chr12:56715600-56722200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:56715600-56722400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:56715600-56722400	Strong transcription	Colonic Mucosa	Colon
41	chr12:56715600-56722600	Strong transcription	Brain Anterior Caudate	brain
42	chr12:56715600-56722800	Strong transcription	Adipose Nuclei	Adipose
43	chr12:56715600-56722800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr12:56715600-56722800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:56715800-56722200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:56715800-56722200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:56715800-56722200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:56715800-56722200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:56715800-56722200	Strong transcription	Fetal Kidney	kidney
50	chr12:56715800-56722200	Strong transcription	Rectal Mucosa Donor 31	rectum

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