Variant report

Variant	rs2723877
Chromosome Location	chr12:104369126-104369127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:104369018-104369543	PBDE	blood:	n/a	n/a
2	MAFF	chr12:104369112-104369473	K562	blood:	n/a	n/a
3	BACH1	chr12:104369066-104369445	K562	blood:	n/a	n/a
4	CEBPD	chr12:104369113-104369637	K562	blood:	n/a	n/a
5	TEAD4	chr12:104369087-104369516	K562	blood:	n/a	n/a
6	YY1	chr12:104369119-104369402	K562	blood:	n/a	n/a
7	POLR2A	chr12:104369104-104369486	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104369091..104370992-chr12:104385433..104387266,2	K562	blood:
2	chr12:104369082..104370853-chr12:104372418..104374505,3	K562	blood:
3	chr12:104324051..104325683-chr12:104367273..104370218,2	K562	blood:

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000166598	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1385663	0.93[CEU][hapmap];0.81[YRI][hapmap]
rs167715	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs167716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2204802	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2248995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2576943	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2576971	1.00[ASN][1000 genomes]
rs2583225	0.93[CEU][hapmap];0.87[TSI][hapmap]
rs2583258	0.85[CEU][hapmap]
rs2583274	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2629750	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs2700494	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2700507	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2700513	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs2700517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2722180	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2722194	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723849	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2723850	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2723853	0.93[CEU][hapmap]
rs322104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs322109	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs784080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs784084	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv3359723	chr12:104359646-104370785	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2723877	JKAMP	trans	parietal	SCAN
rs2723877	ARL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104360800-104371200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:104360800-104371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:104360800-104371200	Weak transcription	Colonic Mucosa	Colon
4	chr12:104360800-104371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104360800-104378600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:104360800-104381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104361000-104370800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:104361000-104371000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:104361000-104371000	Weak transcription	Fetal Kidney	kidney
10	chr12:104361000-104372000	Weak transcription	Stomach Mucosa	stomach
11	chr12:104361200-104369400	Weak transcription	Right Atrium	heart
12	chr12:104361200-104370400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:104361200-104370800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:104361200-104370800	Weak transcription	Fetal Lung	lung
15	chr12:104361200-104371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:104361200-104371000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:104361200-104379400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:104361600-104385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:104361800-104371200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:104362000-104369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:104362000-104373800	Weak transcription	Psoas Muscle	Psoas
22	chr12:104362000-104382600	Weak transcription	Esophagus	oesophagus
23	chr12:104362000-104384400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
25	chr12:104362200-104370800	Weak transcription	Adipose Nuclei	Adipose
26	chr12:104362200-104371200	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:104362200-104384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:104362400-104369200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:104362400-104371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:104362400-104371000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:104362400-104371200	Weak transcription	Brain Germinal Matrix	brain
32	chr12:104362400-104371400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:104362400-104378000	Weak transcription	Small Intestine	intestine
34	chr12:104362600-104371000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:104362600-104371000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:104363200-104370200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:104363200-104371000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:104363400-104371200	Weak transcription	Brain Substantia Nigra	brain
39	chr12:104363400-104371200	Weak transcription	Fetal Brain Female	brain
40	chr12:104363400-104371400	Weak transcription	Spleen	Spleen
41	chr12:104363600-104369800	Weak transcription	Primary T cells from cord blood	blood
42	chr12:104363600-104370600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:104363600-104370600	Weak transcription	HSMMtube	muscle
44	chr12:104363600-104371000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:104363600-104371000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:104363600-104371000	Weak transcription	Gastric	stomach
47	chr12:104363600-104371000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:104363600-104371000	Weak transcription	Thymus	Thymus
49	chr12:104363600-104371200	Weak transcription	Aorta	Aorta
50	chr12:104363600-104371200	Weak transcription	Brain Angular Gyrus	brain

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