Variant report

Variant	rs3754882
Chromosome Location	chr2:99131946-99131947
allele	C/T
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	RCOR1	chr2:99131576-99132095	K562	blood:	n/a	n/a
2	JUND	chr2:99131637-99132235	K562	blood:	n/a	chr2:99131764-99131775 chr2:99131763-99131771 chr2:99131766-99131773 chr2:99131761-99131773
3	MAZ	chr2:99131705-99132017	K562	blood:	n/a	chr2:99131763-99131772

No.	Distal block	Cell Line	Cell type
1	chr2:99029070..99029723-chr2:99131863..99132507,2	MCF-7	breast:
2	chr2:99124187..99127172-chr2:99129019..99132025,3	K562	blood:
3	chr2:99131738..99134767-chr2:99148666..99151301,3	K562	blood:

Variant related genes	Relation type
INPP4A	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs222	0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6542771	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6542805	0.91[ASN][1000 genomes]
rs6542806	0.82[ASN][1000 genomes]
rs6542833	0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007244	chr2:99063753-99136472	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv2840	chr2:99116934-99162190	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99114000-99137600	Weak transcription	Fetal Intestine Large	intestine
2	chr2:99114400-99154000	Weak transcription	HepG2	liver
3	chr2:99115000-99135000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:99116600-99137800	Weak transcription	Fetal Brain Female	brain
5	chr2:99116800-99135600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:99119200-99137400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:99121400-99135800	Weak transcription	Aorta	Aorta
8	chr2:99121600-99155400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:99121800-99136400	Weak transcription	Gastric	stomach
10	chr2:99122200-99135800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:99123200-99154400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:99123600-99134800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:99123800-99136200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:99124200-99134800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:99124600-99137400	Weak transcription	Liver	Liver
16	chr2:99124600-99137600	Weak transcription	Pancreas	Pancrea
17	chr2:99124800-99132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:99124800-99135600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:99125000-99134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:99125200-99144000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:99125400-99137600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:99125400-99143600	Weak transcription	Brain Germinal Matrix	brain
23	chr2:99125600-99134800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:99125600-99136600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:99125600-99140600	Weak transcription	Fetal Heart	heart
26	chr2:99125800-99132200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:99125800-99135800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:99126200-99133800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:99126200-99162000	Weak transcription	Small Intestine	intestine
30	chr2:99126600-99134800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:99126600-99135000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:99127000-99176800	Weak transcription	Right Atrium	heart
33	chr2:99127800-99135200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:99129000-99135200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr2:99129200-99134800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr2:99129400-99135200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:99129600-99134800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:99130000-99132600	Enhancers	Left Ventricle	heart
39	chr2:99130000-99134400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:99130000-99135800	Enhancers	Colon Smooth Muscle	Colon
41	chr2:99130200-99132200	Enhancers	GM12878-XiMat	blood
42	chr2:99130200-99132400	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:99130200-99133000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:99130200-99133000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:99130200-99133400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:99130200-99134000	Weak transcription	Stomach Mucosa	stomach
47	chr2:99130400-99132400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:99130400-99132400	Enhancers	Primary T cells from cord blood	blood
49	chr2:99130400-99132400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:99130400-99132600	Enhancers	Thymus	Thymus

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