Variant report

Variant	rs12621149
Chromosome Location	chr2:128266844-128266845
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:128266133-128266877	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr2:128265851-128266846	A549	lung:	n/a	n/a
3	GATA3	chr2:128265822-128266863	SK-N-SH	brain:	n/a	n/a
4	KAP1	chr2:128265764-128266984	HEK293	kidney:	n/a	n/a
5	NFIC	chr2:128265886-128266889	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr2:128265736-128266846	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128261114..128269570-chr2:128281581..128286258,13	K562	blood:
2	chr2:128266415..128267976-chr2:128271097..128273147,2	MCF-7	breast:
3	chr2:128262614..128267545-chr2:128280339..128284643,6	K562	blood:
4	chr2:128266465..128268562-chr2:128395784..128397620,2	MCF-7	breast:
5	chr2:128255754..128258823-chr2:128264549..128267686,3	K562	blood:
6	chr2:128262034..128264615-chr2:128264870..128267413,2	K562	blood:
7	chr2:128266090..128269191-chr2:128457867..128460953,3	MCF-7	breast:
8	chr2:128266356..128269288-chr2:128281664..128284175,4	MCF-7	breast:

No data

Variant related genes	Relation type
IWS1	TF binding region
ENSG00000173349	Chromatin interaction
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10190872	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10206221	0.87[ASN][1000 genomes]
rs12470481	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12475217	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12987418	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13397441	0.85[ASN][1000 genomes]
rs13399231	0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs13415053	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1549767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015347	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17015399	0.84[ASN][1000 genomes]
rs173013	0.93[ASN][1000 genomes]
rs17522960	0.87[ASN][1000 genomes]
rs1864552	0.81[CEU][hapmap]
rs2078028	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2163348	0.81[CEU][hapmap]
rs2176595	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[ASN][1000 genomes]
rs2249646	0.87[ASN][1000 genomes]
rs2460106	0.81[CEU][hapmap]
rs2566564	0.83[ASN][1000 genomes]
rs2679402	0.97[ASN][1000 genomes]
rs2679407	0.87[ASN][1000 genomes]
rs2679409	0.81[CEU][hapmap]
rs334137	0.81[CEU][hapmap]
rs334138	0.80[CEU][hapmap]
rs334139	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs334140	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs334142	0.87[ASN][1000 genomes]
rs334143	0.81[CEU][hapmap]
rs334144	0.81[CEU][hapmap]
rs334146	0.81[CEU][hapmap]
rs334147	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334148	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334149	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334150	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334151	0.81[CEU][hapmap]
rs334152	0.81[CEU][hapmap]
rs334153	0.97[ASN][1000 genomes]
rs334155	0.97[ASN][1000 genomes]
rs334156	0.81[CEU][hapmap]
rs334158	0.81[CEU][hapmap]
rs334159	0.80[CEU][hapmap]
rs334160	0.81[CEU][hapmap]
rs334162	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3732208	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4423553	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4662582	0.94[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55981410	0.82[ASN][1000 genomes]
rs56217122	0.87[ASN][1000 genomes]
rs56234754	0.83[ASN][1000 genomes]
rs58462277	0.96[ASN][1000 genomes]
rs59934067	0.97[ASN][1000 genomes]
rs61342606	0.83[ASN][1000 genomes]
rs6707186	0.82[ASN][1000 genomes]
rs6707425	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6713317	0.80[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs6722447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727506	0.87[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs6731270	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6734816	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6748790	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6757654	0.83[ASN][1000 genomes]
rs72958594	0.97[ASN][1000 genomes]
rs72958600	0.97[ASN][1000 genomes]
rs7570609	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7572181	0.85[ASN][1000 genomes]
rs7574209	0.87[ASN][1000 genomes]
rs7574215	0.87[ASN][1000 genomes]
rs7576217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7582598	0.81[CEU][hapmap]
rs7598346	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7603777	0.97[ASN][1000 genomes]
rs777547	0.97[ASN][1000 genomes]
rs777549	0.97[ASN][1000 genomes]
rs777550	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs777551	0.97[ASN][1000 genomes]
rs777554	0.81[CEU][hapmap]
rs777557	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs777558	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs777559	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs777561	0.93[ASN][1000 genomes]
rs777562	0.92[ASN][1000 genomes]
rs777563	0.92[ASN][1000 genomes]
rs777569	0.81[CEU][hapmap]
rs9287540	0.90[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12621149	ERCC3	cis	cerebellum	SCAN
rs12621149	MAP3K2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128235200-128270000	Strong transcription	Dnd41	blood
3	chr2:128246200-128271800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:128263000-128267600	Weak transcription	Stomach Mucosa	stomach
6	chr2:128263000-128272000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
8	chr2:128263200-128267000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:128263200-128267400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:128263200-128268600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:128263200-128268600	Weak transcription	Thymus	Thymus
12	chr2:128263200-128268800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:128263200-128269400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:128263200-128271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:128263200-128271400	Weak transcription	Colonic Mucosa	Colon
16	chr2:128263200-128271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:128263200-128271600	Weak transcription	Pancreas	Pancrea
18	chr2:128263200-128271600	Weak transcription	Spleen	Spleen
19	chr2:128263200-128271800	Weak transcription	Aorta	Aorta
20	chr2:128263200-128271800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:128263200-128271800	Weak transcription	Esophagus	oesophagus
22	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:128263400-128268000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:128263400-128268600	Weak transcription	Fetal Thymus	thymus
25	chr2:128263400-128269600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:128263400-128271600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:128263400-128271600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:128263400-128271800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:128263400-128271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:128263400-128275400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:128263800-128267800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:128263800-128269800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:128264200-128267000	Enhancers	Brain Substantia Nigra	brain
34	chr2:128264200-128267200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:128264200-128267200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:128264200-128267400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:128264200-128268200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:128264400-128267400	Enhancers	Brain Hippocampus Middle	brain
39	chr2:128264400-128267800	Enhancers	Colon Smooth Muscle	Colon
40	chr2:128264400-128268000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:128264400-128268200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:128264600-128267000	Enhancers	Brain Angular Gyrus	brain
43	chr2:128264600-128267800	Enhancers	Liver	Liver
44	chr2:128264600-128270200	Enhancers	Fetal Intestine Small	intestine
45	chr2:128265000-128267200	Enhancers	Hela-S3	cervix
46	chr2:128265000-128267400	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:128265200-128267200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:128265200-128267200	Enhancers	HUVEC	blood vessel
49	chr2:128265400-128267400	Enhancers	HSMM	muscle
50	chr2:128265600-128267000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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