Variant report

Variant	rs2334961
Chromosome Location	chr3:52173625-52173626
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52173481..52175976-chr3:52179788..52182229,2	MCF-7	breast:
2	chr3:52026096..52028947-chr3:52173334..52176505,3	K562	blood:
3	chr3:52168843..52170779-chr3:52171993..52173703,2	K562	blood:
4	chr3:51997651..51999473-chr3:52171714..52174151,2	K562	blood:
5	chr3:51976205..51978258-chr3:52172290..52174891,2	K562	blood:
6	chr3:52172486..52174028-chr3:52174785..52177207,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12386365	0.85[AFR][1000 genomes]
rs12495536	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs12496447	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629791	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28387060	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452586	0.82[AFR][1000 genomes]
rs2878438	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352152	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687607	0.93[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773704	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777340	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778442	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786592	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731684	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs735768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747343	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616695	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644325	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs876782	0.89[YRI][hapmap]
rs893055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809254	0.89[YRI][hapmap]
rs9828327	1.00[CEU][hapmap];0.97[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843852	0.86[YRI][hapmap]
rs9846049	0.89[YRI][hapmap]
rs9851576	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9874939	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:52140400-52178200	Strong transcription	Dnd41	blood
4	chr3:52148600-52179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52155200-52180000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52155200-52187200	Weak transcription	Colonic Mucosa	Colon
7	chr3:52156200-52178000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:52156200-52187600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:52156600-52177800	Weak transcription	Fetal Brain Female	brain
10	chr3:52157200-52187600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:52157400-52178200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:52157400-52187200	Weak transcription	Fetal Kidney	kidney
13	chr3:52157600-52178600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52160200-52179600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:52160600-52182600	Weak transcription	NHDF-Ad	bronchial
16	chr3:52161200-52176400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:52161400-52178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:52162400-52184800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:52162800-52176400	Weak transcription	Placenta	Placenta
20	chr3:52162800-52176400	Weak transcription	HMEC	breast
21	chr3:52162800-52179400	Weak transcription	A549	lung
22	chr3:52162800-52187000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:52162800-52187200	Weak transcription	NH-A	brain
24	chr3:52163000-52176600	Weak transcription	K562	blood
25	chr3:52163200-52177400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:52163400-52185000	Strong transcription	Thymus	Thymus
27	chr3:52163600-52176600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52164800-52174400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:52167000-52178200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:52167200-52185200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:52167600-52177800	Weak transcription	Esophagus	oesophagus
32	chr3:52167600-52179800	Weak transcription	Fetal Lung	lung
33	chr3:52167800-52177200	Strong transcription	Fetal Thymus	thymus
34	chr3:52169000-52178200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:52169000-52185000	Strong transcription	Fetal Intestine Small	intestine
36	chr3:52169200-52173800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:52169200-52178000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:52169200-52178000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:52169200-52184200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:52169200-52185000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:52169400-52176800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:52169600-52184600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:52169600-52185000	Strong transcription	NHLF	lung
44	chr3:52169600-52186600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52169800-52175200	Weak transcription	GM12878-XiMat	blood
46	chr3:52169800-52178000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:52169800-52185200	Strong transcription	Fetal Stomach	stomach
48	chr3:52170000-52173800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr3:52170000-52177400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:52170800-52178200	Weak transcription	Stomach Smooth Muscle	stomach

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