Variant report

Variant	rs2296125
Chromosome Location	chr10:6441591-6441592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6319800..6323554-chr10:6441503..6444162,3	MCF-7	breast:
2	chr10:6268377..6270952-chr10:6439615..6442494,2	MCF-7	breast:
3	chr10:6336971..6341697-chr10:6441247..6445868,11	MCF-7	breast:
4	chr10:6335347..6345426-chr10:6438966..6446500,25	MCF-7	breast:
5	chr10:6405295..6407901-chr10:6440170..6443280,3	MCF-7	breast:
6	chr10:6355714..6359747-chr10:6439655..6444608,4	MCF-7	breast:
7	chr10:6256631..6260538-chr10:6441320..6445135,3	MCF-7	breast:
8	chr10:6242682..6246426-chr10:6435409..6441608,6	MCF-7	breast:
9	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
10	chr10:6213842..6217578-chr10:6440215..6444300,4	MCF-7	breast:
11	chr10:6433781..6435958-chr10:6440894..6443926,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000226705	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10508308	1.00[CEU][hapmap]
rs10906420	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10906426	0.84[ASN][1000 genomes]
rs10906429	0.86[ASW][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11258461	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11258500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11258501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11258515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11258589	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11596750	0.92[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12413588	0.84[CHB][hapmap]
rs12572911	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17155850	0.85[CEU][hapmap]
rs17155855	0.85[CEU][hapmap]
rs2236380	0.92[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs2296126	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs35935618	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3793725	0.85[CEU][hapmap]
rs3793726	0.85[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs590467	0.85[CEU][hapmap]
rs631968	0.92[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs658648	0.89[ASN][1000 genomes]
rs681604	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs688853	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs71479777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7916702	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs7918923	0.85[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs961203	0.85[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs9633784	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6425600-6443600	Weak transcription	Aorta	Aorta
2	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
3	chr10:6434600-6443600	Weak transcription	Fetal Brain Female	brain
4	chr10:6436400-6443600	Weak transcription	Fetal Kidney	kidney
5	chr10:6436600-6443400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:6436600-6443400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:6437200-6444000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr10:6437600-6444400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:6438600-6441600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:6439200-6443400	Weak transcription	NHEK	skin
11	chr10:6440400-6442000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr10:6440400-6443400	Enhancers	Brain Substantia Nigra	brain
13	chr10:6440400-6443600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:6440600-6442000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:6440600-6442200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:6440600-6443600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr10:6440600-6444000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr10:6440800-6442000	Enhancers	Primary B cells from cord blood	blood
19	chr10:6440800-6442200	Enhancers	Fetal Stomach	stomach
20	chr10:6440800-6443600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr10:6440800-6443600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:6441000-6441600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:6441000-6441600	Enhancers	HMEC	breast
24	chr10:6441000-6441800	Enhancers	NHLF	lung
25	chr10:6441000-6442200	Enhancers	Placenta	Placenta
26	chr10:6441000-6442200	Enhancers	Stomach Smooth Muscle	stomach
27	chr10:6441000-6442200	Enhancers	NH-A	brain
28	chr10:6441000-6442400	Flanking Active TSS	A549	lung
29	chr10:6441000-6442600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:6441000-6442800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr10:6441000-6443800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:6441200-6441600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:6441200-6441800	Weak transcription	Fetal Thymus	thymus
34	chr10:6441200-6442200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:6441200-6442200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:6441200-6443400	Weak transcription	Adipose Nuclei	Adipose
37	chr10:6441200-6443400	Enhancers	Brain Anterior Caudate	brain
38	chr10:6441200-6443600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr10:6441200-6443600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr10:6441200-6443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr10:6441400-6441600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr10:6441400-6441600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:6441400-6442000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:6441400-6442000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr10:6441400-6442000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr10:6441400-6442000	Enhancers	Fetal Brain Male	brain
47	chr10:6441400-6442000	Enhancers	Dnd41	blood
48	chr10:6441400-6442200	Enhancers	Fetal Lung	lung
49	chr10:6441400-6442200	Enhancers	Fetal Muscle Leg	muscle
50	chr10:6441400-6442400	Enhancers	Lung	lung

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