Variant report

Variant	rs33054
Chromosome Location	chr3:159602263-159602264
allele	A/C
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	CTCF	chr3:159602260-159602410	GM12865	blood:	n/a	n/a
2	CTCF	chr3:159602260-159602410	GM12864	blood:	n/a	n/a
3	CTCF	chr3:159602240-159602390	HMEC	breast:	n/a	n/a
4	CTCF	chr3:159602174-159603599	A549	lung:	n/a	chr3:159602772-159602793 chr3:159602771-159602787 chr3:159602770-159602788
5	RAD21	chr3:159599160-159603476	SK-N-SH	brain:	n/a	chr3:159600668-159600682 chr3:159600519-159600531 chr3:159601277-159601291
6	CTCF	chr3:159602077-159603315	SK-N-SH	brain:	n/a	chr3:159602772-159602793 chr3:159602771-159602787 chr3:159602770-159602788
7	SMC3	chr3:159602215-159604155	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:159546081..159548652-chr3:159599760..159602729,2	MCF-7	breast:
2	chr3:159602113..159604329-chr3:159720537..159722903,2	MCF-7	breast:
3	chr3:159602039..159602804-chr3:159721053..159721805,2	MCF-7	breast:

Variant related genes	Relation type
SCHIP1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13070254	1.00[JPT][hapmap]
rs1461103	1.00[JPT][hapmap]
rs1463514	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1675497	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2126143	1.00[JPT][hapmap]
rs2169303	1.00[JPT][hapmap]
rs26298	0.92[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2886623	1.00[JPT][hapmap]
rs33050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33056	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863075	1.00[JPT][hapmap]
rs3911714	1.00[JPT][hapmap]
rs4513503	1.00[JPT][hapmap]
rs6441275	1.00[JPT][hapmap]
rs7636819	1.00[JPT][hapmap]

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	nsv877698	chr3:159583518-159640152	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv997776	chr3:159585097-159668421	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159588200-159605200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:159590800-159617600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:159593400-159605400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:159594000-159606600	Weak transcription	Fetal Kidney	kidney
5	chr3:159596200-159613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:159597000-159605800	Enhancers	Brain Angular Gyrus	brain
7	chr3:159598800-159602800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:159599200-159603200	Enhancers	HUVEC	blood vessel
9	chr3:159599400-159603600	Enhancers	Colon Smooth Muscle	Colon
10	chr3:159599800-159609400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:159599800-159620400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:159600000-159610200	Weak transcription	Esophagus	oesophagus
13	chr3:159600000-159610200	Weak transcription	A549	lung
14	chr3:159600400-159605000	Weak transcription	Aorta	Aorta
15	chr3:159600400-159605400	Weak transcription	Adipose Nuclei	Adipose
16	chr3:159600800-159603800	Enhancers	Brain Anterior Caudate	brain
17	chr3:159600800-159604000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:159600800-159604200	Enhancers	Fetal Heart	heart
19	chr3:159600800-159609400	Weak transcription	Fetal Brain Female	brain
20	chr3:159601000-159603800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:159601000-159606000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr3:159601000-159610200	Weak transcription	Placenta	Placenta
23	chr3:159601200-159604200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:159601200-159604400	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:159601200-159607200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:159601200-159609800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:159601200-159609800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:159601200-159609800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:159601200-159610000	Weak transcription	Spleen	Spleen
30	chr3:159601200-159610200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:159601200-159615200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:159601400-159602400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:159601400-159602600	Weak transcription	Fetal Stomach	stomach
34	chr3:159601400-159602600	Weak transcription	Left Ventricle	heart
35	chr3:159601400-159602600	Weak transcription	Psoas Muscle	Psoas
36	chr3:159601400-159602600	Weak transcription	Right Atrium	heart
37	chr3:159601400-159602600	Weak transcription	Right Ventricle	heart
38	chr3:159601400-159603000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:159601400-159603000	Weak transcription	Brain Germinal Matrix	brain
40	chr3:159601400-159603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:159601400-159603200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:159601400-159603200	Enhancers	Osteobl	bone
43	chr3:159601400-159603400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:159601400-159603800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:159601400-159604200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:159601400-159604400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:159601400-159604600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:159601400-159605000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:159601400-159605400	Enhancers	Brain Cingulate Gyrus	brain
50	chr3:159601400-159605400	Enhancers	Brain Substantia Nigra	brain

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