Variant report

Variant	rs10931229
Chromosome Location	chr2:153516809-153516810
allele	C/G
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	chr2:153516664-153517233	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:153516738-153518383	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153509462..153511338-chr2:153515994..153518973,2	K562	blood:
2	chr2:153516162..153518944-chr2:153526329..153528091,2	MCF-7	breast:
3	chr2:153516775..153519458-chr2:153520976..153522617,2	K562	blood:

Variant related genes	Relation type
PRPF40A	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10172024	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10181485	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200667	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1036526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1065266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1128804	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11544718	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11899051	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12477881	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12621561	0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12693415	0.85[CHB][hapmap]
rs12997814	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13005368	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13010731	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13017428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13417781	0.81[CHB][hapmap]
rs13419068	0.86[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1370498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831740	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17328734	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17400645	0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1962313	0.80[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1986743	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1992146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304556	0.90[CHB][hapmap]
rs2304559	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2346534	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2346539	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2346540	0.88[ASN][1000 genomes]
rs2346541	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346542	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346543	0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2346549	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2346550	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3171980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3175	0.84[JPT][hapmap]
rs34585982	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34668102	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748937	0.86[ASN][1000 genomes]
rs3748938	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3748939	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762503	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs3762506	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3811566	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233660	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4267470	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4664121	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4664122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664601	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs4664602	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664604	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664605	0.80[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4664606	0.80[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4664607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664609	0.85[ASN][1000 genomes]
rs4664610	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs55785027	0.86[EUR][1000 genomes]
rs56283545	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6434128	0.95[CHB][hapmap]
rs6434161	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434162	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713779	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723574	0.82[ASN][1000 genomes]
rs6727279	0.87[ASN][1000 genomes]
rs6746079	0.88[ASN][1000 genomes]
rs6746321	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748160	0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs715047	0.88[ASN][1000 genomes]
rs72871191	0.88[ASN][1000 genomes]
rs72872607	0.88[ASN][1000 genomes]
rs7556673	0.86[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7558920	0.83[ASN][1000 genomes]
rs7559219	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7560393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7570759	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7576152	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7576847	0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs7582253	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7592669	0.94[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596408	0.85[CHB][hapmap]
rs7599946	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7605709	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608603	0.80[CHB][hapmap];0.86[ASN][1000 genomes]
rs9288121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9288127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9646744	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9789505	0.88[ASN][1000 genomes]
rs9789521	0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:153495400-153517400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:153497000-153531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:153497200-153521200	Weak transcription	Esophagus	oesophagus
5	chr2:153500400-153517200	Weak transcription	Hela-S3	cervix
6	chr2:153501400-153531800	Weak transcription	Aorta	Aorta
7	chr2:153504400-153538200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:153505000-153517400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:153505000-153517400	Weak transcription	Gastric	stomach
10	chr2:153505000-153517400	Weak transcription	Right Ventricle	heart
11	chr2:153505000-153540200	Strong transcription	Fetal Thymus	thymus
12	chr2:153505400-153517000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153505400-153539200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:153505400-153540200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:153505600-153534400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:153505600-153537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:153505600-153538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:153506000-153538000	Strong transcription	Liver	Liver
19	chr2:153506200-153539800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:153506200-153546800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:153507000-153523000	Strong transcription	HUVEC	blood vessel
22	chr2:153507000-153538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:153507000-153541600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:153507200-153538200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:153507400-153530200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:153507600-153526800	Weak transcription	Stomach Mucosa	stomach
27	chr2:153508000-153542000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:153508000-153550800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:153508200-153532800	Strong transcription	HSMM	muscle
30	chr2:153508200-153533600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:153508400-153517800	Strong transcription	HepG2	liver
32	chr2:153508400-153537600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:153508400-153537800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:153508400-153538000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:153508400-153538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:153508400-153538400	Strong transcription	A549	lung
37	chr2:153508600-153529200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:153508600-153539600	Strong transcription	Dnd41	blood
39	chr2:153508800-153535000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:153508800-153540400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:153509000-153539600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:153509200-153520800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:153509200-153521400	Strong transcription	Placenta	Placenta
44	chr2:153509200-153551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:153509400-153538400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:153509800-153535000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:153509800-153540000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:153510000-153530200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:153510400-153539400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:153510400-153539600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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