Variant report

Variant	rs1001856
Chromosome Location	chr2:99185423-99185424
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:99185068-99185468	K562	blood:	n/a	n/a
2	CTCF	chr2:99185320-99185470	NHEK	skin:	n/a	n/a
3	CTCF	chr2:99185280-99185430	HCM	heart:	n/a	n/a
4	CTCF	chr2:99185340-99186016	GM19239	blood:	n/a	chr2:99185894-99185915
5	CTCF	chr2:99185418-99186160	SK-N-SH	brain:	n/a	chr2:99185894-99185915
6	CTCF	chr2:99185416-99185425	GM12892	blood:	n/a	n/a
7	SMC3	chr2:99185343-99186232	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr2:99185417-99185431	NHEK	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:98912225..98912826-chr2:99185396..99186137,2	MCF-7	breast:
2	chr2:99059933..99062101-chr2:99184919..99186456,2	MCF-7	breast:
3	chr2:99185380..99185885-chr2:99682836..99683668,2	MCF-7	breast:
4	chr2:99185410..99186274-chr2:99196194..99197004,2	MCF-7	breast:
5	chr2:99185377..99186027-chr2:99217737..99218658,5	MCF-7	breast:
6	chr2:99104311..99105013-chr2:99185338..99186009,2	K562	blood:
7	chr2:99185336..99186312-chr2:99217722..99218655,3	MCF-7	breast:

No data

Variant related genes	Relation type
INPP4A	TF binding region
ENSG00000040933	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10201079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995531	1.00[YRI][hapmap]
rs2174354	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754874	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820947	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851143	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542781	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7559530	1.00[YRI][hapmap]
rs7604208	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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	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
2	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
3	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99147200-99200200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:99148400-99211200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:99149000-99209800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:99149000-99210800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:99149200-99210800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:99156400-99197000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:99158800-99190600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:99159800-99201600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:99163000-99215000	Weak transcription	HMEC	breast
10	chr2:99163800-99194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:99164400-99210800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:99167600-99193400	Weak transcription	Fetal Heart	heart
13	chr2:99168000-99205200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:99168400-99210400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:99168600-99197600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:99169400-99222600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:99173000-99186000	Weak transcription	Stomach Mucosa	stomach
18	chr2:99173200-99205000	Strong transcription	Primary T cells from cord blood	blood
19	chr2:99173400-99204800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:99174000-99204000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:99174600-99207800	Weak transcription	HUVEC	blood vessel
22	chr2:99176000-99205400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:99176200-99203400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:99176200-99210600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:99176400-99205200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:99177200-99190800	Strong transcription	Brain Anterior Caudate	brain
27	chr2:99177400-99201600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:99177400-99210800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:99177400-99213000	Weak transcription	NHDF-Ad	bronchial
30	chr2:99177400-99216200	Weak transcription	NH-A	brain
31	chr2:99177400-99221000	Weak transcription	Psoas Muscle	Psoas
32	chr2:99178200-99201400	Strong transcription	Fetal Stomach	stomach
33	chr2:99178600-99186200	Genic enhancers	Fetal Thymus	thymus
34	chr2:99178600-99186600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:99178600-99189800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:99178600-99190600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:99178800-99193800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:99178800-99201200	Strong transcription	Spleen	Spleen
39	chr2:99179000-99186600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:99179200-99196600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:99179400-99186600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:99179400-99190000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:99179400-99190400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:99179400-99190600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:99179400-99198600	Strong transcription	Fetal Intestine Small	intestine
46	chr2:99179400-99204200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:99179600-99186600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:99179600-99186600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:99179600-99190200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:99179600-99195400	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links