Variant report

Variant	rs2961570
Chromosome Location	chr10:4870644-4870645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:4868054-4871160	K562	blood:	n/a	n/a
2	CUX1	chr10:4869837-4870752	K562	blood:	n/a	n/a
3	TBL1XR1	chr10:4870159-4870973	K562	blood:	n/a	n/a
4	CCNT2	chr10:4870120-4870655	K562	blood:	n/a	n/a
5	ARID3A	chr10:4869242-4871035	K562	blood:	n/a	n/a
6	RCOR1	chr10:4869971-4870757	K562	blood:	n/a	n/a
7	RCOR1	chr10:4870222-4870746	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:4861761..4864684-chr10:4870409..4873110,2	K562	blood:
2	chr10:4868628..4871525-chr10:4902310..4904323,2	K562	blood:
3	chr10:4869791..4871610-chr10:4890458..4893097,2	K562	blood:
4	chr10:4866839..4870831-chr10:5488473..5491962,3	MCF-7	breast:
5	chr10:4869493..4871695-chr10:5409479..5411082,2	K562	blood:
6	chr10:4866089..4871671-chr10:4873094..4876081,6	MCF-7	breast:
7	chr10:4869313..4873235-chr10:4874956..4878368,5	K562	blood:
8	chr10:4867330..4870814-chr10:4881434..4885680,3	K562	blood:
9	chr10:4867480..4871698-chr10:4879074..4886734,7	K562	blood:
10	chr10:4869756..4872068-chr10:4996333..4999086,2	MCF-7	breast:
11	chr10:4869978..4871994-chr10:5334140..5336719,2	K562	blood:
12	chr10:4869420..4871876-chr10:5136948..5139293,2	K562	blood:

No data

Variant related genes	Relation type
AKR1E2	TF binding region
ENSG00000173848	Chromatin interaction
ENSG00000196139	Chromatin interaction
ENSG00000165568	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs12569410	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs12569715	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12569839	0.86[ASN][1000 genomes]
rs12570011	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12570641	0.86[ASN][1000 genomes]
rs12571065	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12571192	0.86[ASN][1000 genomes]
rs12571212	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12571543	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12571691	0.86[ASN][1000 genomes]
rs12571940	0.86[ASN][1000 genomes]
rs12571967	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12571976	0.86[ASN][1000 genomes]
rs12571980	0.86[ASN][1000 genomes]
rs12572008	0.86[ASN][1000 genomes]
rs12572181	0.86[ASN][1000 genomes]
rs12573010	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12573159	0.86[ASN][1000 genomes]
rs12573197	0.86[ASN][1000 genomes]
rs12573397	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12573398	0.86[ASN][1000 genomes]
rs12573501	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs12573669	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12573690	0.86[ASN][1000 genomes]
rs12573808	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133680	0.80[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133691	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs17133693	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133697	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133705	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133710	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs17133724	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133747	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs17133748	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133751	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133752	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133753	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133759	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133762	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133779	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133780	0.86[ASN][1000 genomes]
rs17133791	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133794	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17133796	0.86[ASN][1000 genomes]
rs1869214	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1869215	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1869216	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1869217	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1869219	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1869220	0.86[ASN][1000 genomes]
rs1901642	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1901645	0.83[MKK][hapmap]
rs1993182	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2278869	0.86[ASN][1000 genomes]
rs2290348	0.86[ASN][1000 genomes]
rs2290349	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2290350	0.86[ASN][1000 genomes]
rs2397982	0.86[ASN][1000 genomes]
rs2397983	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2397985	0.86[ASN][1000 genomes]
rs2397986	0.86[ASN][1000 genomes]
rs2924269	0.81[MKK][hapmap]
rs2924274	0.98[AFR][1000 genomes]
rs2924275	0.97[ASN][1000 genomes]
rs2924277	0.84[MKK][hapmap]
rs2924278	0.87[MKK][hapmap]
rs2961569	0.94[AFR][1000 genomes]
rs2961572	0.98[AFR][1000 genomes]
rs2961573	0.98[AFR][1000 genomes]
rs2961585	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs34882719	0.86[ASN][1000 genomes]
rs35340010	0.86[ASN][1000 genomes]
rs3750737	0.86[ASN][1000 genomes]
rs3750738	0.86[ASN][1000 genomes]
rs3750739	0.86[ASN][1000 genomes]
rs3750740	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs41289263	0.86[ASN][1000 genomes]
rs4242772	0.84[MKK][hapmap]
rs4317889	0.88[MKK][hapmap]
rs4339941	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4397733	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4480435	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4518987	0.86[ASN][1000 genomes]
rs4593903	0.86[ASN][1000 genomes]
rs7090869	0.86[MKK][hapmap]
rs72478258	0.84[ASN][1000 genomes]
rs7912440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2961570	AKR1C1	cis	parietal	SCAN
rs2961570	AKR1E2	cis	cerebellum	SCAN
rs2961570	AKR1C1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4868800-4874600	Weak transcription	Spleen	Spleen
2	chr10:4868800-4879800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:4869000-4875000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:4869000-4881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:4869200-4872800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:4869200-4873400	Weak transcription	Fetal Stomach	stomach
7	chr10:4869200-4874000	Weak transcription	Lung	lung
8	chr10:4869200-4875400	Weak transcription	Ovary	ovary
9	chr10:4869200-4875600	Weak transcription	Gastric	stomach
10	chr10:4869200-4876600	Weak transcription	Fetal Brain Female	brain
11	chr10:4869200-4877600	Weak transcription	Pancreas	Pancrea
12	chr10:4869200-4877800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:4869200-4883600	Weak transcription	Thymus	Thymus
14	chr10:4869200-4884800	Weak transcription	Esophagus	oesophagus
15	chr10:4869200-4889200	Weak transcription	NHLF	lung
16	chr10:4869200-4889600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:4869200-4890400	Weak transcription	Right Atrium	heart
18	chr10:4869200-4891600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:4869200-4892200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:4869400-4873000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:4869400-4873000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:4869400-4873000	Weak transcription	Fetal Muscle Leg	muscle
23	chr10:4869400-4873000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:4869400-4873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:4869400-4873400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:4869400-4876000	Weak transcription	Brain Germinal Matrix	brain
27	chr10:4869400-4877200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:4869400-4877600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:4869400-4878400	Weak transcription	Placenta	Placenta
30	chr10:4869400-4879000	Weak transcription	Fetal Lung	lung
31	chr10:4869400-4883400	Weak transcription	Colonic Mucosa	Colon
32	chr10:4869400-4886800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:4869400-4889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:4869400-4889600	Weak transcription	HSMM	muscle
35	chr10:4869400-4891600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr10:4869600-4871000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:4869600-4872400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:4869600-4872800	Weak transcription	Aorta	Aorta
39	chr10:4869600-4872800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr10:4869600-4873000	Weak transcription	Adipose Nuclei	Adipose
41	chr10:4869600-4873000	Weak transcription	Fetal Kidney	kidney
42	chr10:4869600-4873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:4869600-4875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:4869600-4875600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr10:4869600-4877000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr10:4869600-4877200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:4869600-4877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr10:4869600-4877600	Weak transcription	Osteobl	bone
49	chr10:4869600-4878600	Weak transcription	Colon Smooth Muscle	Colon
50	chr10:4869600-4883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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