Variant report

Variant	rs3815877
Chromosome Location	chr2:182783848-182783849
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	POLR2A	chr2:182778854-182784341	HCT-116	colon:	n/a	n/a
2	POLR2A	chr2:182783417-182784275	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:182780635-182784508	K562	blood:	n/a	n/a
4	POLR2A	chr2:182783753-182784114	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:182779182-182784349	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:182772464..182776872-chr2:182781009..182784749,5	K562	blood:
2	chr2:182782249..182784945-chr2:182785001..182787819,5	MCF-7	breast:

Variant related genes	Relation type
SSFA2	TF binding region
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10166975	0.84[EUR][1000 genomes]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10189187	0.87[EUR][1000 genomes]
rs10191082	0.84[EUR][1000 genomes]
rs10197254	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13389121	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13401364	0.87[EUR][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1528025	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1528026	0.84[EUR][1000 genomes]
rs1528027	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16867498	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16867509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17456384	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881158	1.00[CEU][hapmap]
rs1881159	1.00[CEU][hapmap]
rs2059702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2368224	1.00[CEU][hapmap]
rs2368235	0.88[EUR][1000 genomes]
rs3731693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597477	0.84[EUR][1000 genomes]
rs55732891	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55758877	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6707654	0.84[EUR][1000 genomes]
rs6720109	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6720702	1.00[CEU][hapmap]
rs6723011	0.84[EUR][1000 genomes]
rs6735322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6736341	0.84[EUR][1000 genomes]
rs6736766	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6739707	0.84[EUR][1000 genomes]
rs6744556	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751464	0.84[EUR][1000 genomes]
rs6751685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754819	0.84[EUR][1000 genomes]
rs6755017	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73032623	0.87[EUR][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7563333	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580410	1.00[CEU][hapmap]
rs7603721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606321	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7608942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9807949	1.00[CEU][hapmap]
rs9808112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182757800-182790400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:182759800-182789400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:182760000-182794800	Strong transcription	Fetal Thymus	thymus
4	chr2:182760800-182787000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:182761400-182795800	Strong transcription	Placenta	Placenta
6	chr2:182764600-182786600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:182768200-182787800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:182769400-182795600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:182769600-182795800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:182769600-182795800	Strong transcription	Dnd41	blood
11	chr2:182772400-182790800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:182774000-182790800	Strong transcription	HMEC	breast
13	chr2:182774600-182787400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:182774600-182788400	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:182774600-182795200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:182775000-182788800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:182775800-182792200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr2:182775800-182792600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:182775800-182795800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:182775800-182795800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:182776000-182795800	Strong transcription	Hela-S3	cervix
22	chr2:182776200-182793200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:182776400-182785400	Strong transcription	A549	lung
24	chr2:182776400-182787600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:182776800-182791600	Strong transcription	Fetal Intestine Large	intestine
26	chr2:182777200-182788400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:182778200-182784200	Genic enhancers	Liver	Liver
28	chr2:182778200-182788000	Strong transcription	K562	blood
29	chr2:182778200-182788200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:182778800-182788000	Strong transcription	Fetal Lung	lung
31	chr2:182778800-182792800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:182778800-182792800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr2:182779000-182784400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:182779000-182784400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:182779000-182784400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:182779000-182784800	Strong transcription	Colon Smooth Muscle	Colon
37	chr2:182779000-182787000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:182779000-182787200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr2:182779000-182787400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:182779000-182787600	Strong transcription	Primary T cells from cord blood	blood
41	chr2:182779000-182787600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:182779000-182787600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:182779000-182787600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:182779000-182788000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:182779000-182788200	Strong transcription	Fetal Kidney	kidney
46	chr2:182779000-182790800	Strong transcription	HSMMtube	muscle
47	chr2:182779200-182784200	Strong transcription	Colonic Mucosa	Colon
48	chr2:182779200-182784800	Strong transcription	GM12878-XiMat	blood
49	chr2:182779200-182787600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:182779200-182788200	Strong transcription	Primary B cells from cord blood	blood

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