Variant report

Variant	rs7628235
Chromosome Location	chr3:42546477-42546478
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42530093..42535343-chr3:42545492..42550064,6	MCF-7	breast:
3	chr3:42518552..42520973-chr3:42544499..42546784,2	MCF-7	breast:
4	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1078008	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1511955	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1876504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55886057	1.00[EUR][1000 genomes]
rs56184136	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441862	0.84[ASN][1000 genomes]
rs73082655	0.83[EUR][1000 genomes]
rs755082	1.00[MEX][hapmap];0.89[YRI][hapmap]
rs7613206	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615762	0.85[YRI][hapmap]
rs7628932	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651400	0.91[EUR][1000 genomes]
rs9867564	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42544000-42546600	Enhancers	Spleen	Spleen
2	chr3:42544600-42548800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
4	chr3:42544800-42548400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:42544800-42548600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42544800-42548600	Weak transcription	Esophagus	oesophagus
7	chr3:42544800-42548800	Weak transcription	Left Ventricle	heart
8	chr3:42544800-42548800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:42544800-42550600	Weak transcription	Right Atrium	heart
10	chr3:42545000-42547400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:42545000-42547400	Weak transcription	Right Ventricle	heart
12	chr3:42545000-42547600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:42545000-42548600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:42545000-42548600	Weak transcription	Liver	Liver
15	chr3:42545000-42548800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:42545000-42549800	Weak transcription	Small Intestine	intestine
17	chr3:42545200-42546600	Active TSS	Adipose Nuclei	Adipose
18	chr3:42545200-42547000	Active TSS	Lung	lung
19	chr3:42545200-42547000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:42545200-42547600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:42545200-42548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:42545200-42548800	Weak transcription	NHEK	skin
23	chr3:42545400-42546800	Enhancers	K562	blood
24	chr3:42545400-42547400	Enhancers	Stomach Mucosa	stomach
25	chr3:42545400-42549000	Enhancers	Primary T cells from cord blood	blood
26	chr3:42545400-42551400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:42545600-42546600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:42545600-42547000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:42545600-42547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:42545600-42548600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:42545600-42548600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:42545600-42548800	Weak transcription	Gastric	stomach
34	chr3:42545600-42550200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:42545800-42546800	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr3:42545800-42547000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:42545800-42547400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:42545800-42547400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:42545800-42547800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:42545800-42548400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:42545800-42548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:42545800-42549000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:42545800-42549000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:42546000-42546600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr3:42546000-42547800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:42546000-42549400	Weak transcription	Brain Anterior Caudate	brain
47	chr3:42546200-42546600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:42546200-42546600	Genic enhancers	Fetal Intestine Small	intestine
49	chr3:42546200-42547000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:42546200-42548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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