Variant report

Variant	rs3888014
Chromosome Location	chr1:9923486-9923487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9882600..9885826-chr1:9921034..9924372,4	MCF-7	breast:
2	chr1:9921008..9924998-chr1:9925415..9929659,6	K562	blood:
3	chr1:9881352..9884024-chr1:9922177..9924275,2	K562	blood:
4	chr1:9921625..9924250-chr1:9926048..9928989,2	K562	blood:
5	chr1:9907349..9914090-chr1:9919874..9926540,9	K562	blood:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction
ENSG00000223989	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11121499	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11809921	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220392	0.84[CHB][hapmap]
rs1220396	0.84[CHB][hapmap]
rs1220405	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs1220408	0.95[ASN][1000 genomes]
rs1220412	0.82[CHD][hapmap]
rs1220418	0.84[CHB][hapmap]
rs15177	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17034420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033960	0.86[EUR][1000 genomes]
rs2278611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860318	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56315207	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57979292	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58281392	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59341676	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59530761	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59533551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60389428	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60547803	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60624175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785229	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61785586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785590	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658583	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6683824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695334	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858068	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74054138	0.85[AMR][1000 genomes]
rs7529783	0.85[AMR][1000 genomes]
rs7533225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs935073	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs935075	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs946275	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
2	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
3	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
5	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:9904600-9935000	Weak transcription	Osteobl	bone
7	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
8	chr1:9906600-9927400	Weak transcription	Liver	Liver
9	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:9907400-9929800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:9910000-9935000	Weak transcription	NHLF	lung
12	chr1:9911000-9927400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:9911000-9930400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:9911200-9932400	Weak transcription	Fetal Heart	heart
15	chr1:9911400-9927200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:9912200-9929600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:9912200-9929600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:9912600-9927000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:9913200-9923600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:9913400-9927400	Weak transcription	Fetal Brain Male	brain
21	chr1:9913600-9923600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:9913600-9927800	Weak transcription	Brain Angular Gyrus	brain
23	chr1:9914000-9927200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:9914000-9927400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:9914000-9927400	Weak transcription	Dnd41	blood
26	chr1:9914000-9927800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:9914000-9929600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:9914000-9929800	Weak transcription	Primary T cells from cord blood	blood
29	chr1:9914200-9926800	Weak transcription	Fetal Lung	lung
30	chr1:9915800-9928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:9917800-9925200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
34	chr1:9918000-9932800	Strong transcription	Fetal Brain Female	brain
35	chr1:9918200-9924400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:9918200-9932800	Strong transcription	Lung	lung
37	chr1:9918400-9923600	Weak transcription	Psoas Muscle	Psoas
38	chr1:9918600-9923600	Strong transcription	Fetal Stomach	stomach
39	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
40	chr1:9918800-9925800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:9919400-9926000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:9919800-9924200	Strong transcription	Gastric	stomach
43	chr1:9919800-9924800	Weak transcription	HUVEC	blood vessel
44	chr1:9919800-9926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:9920000-9923600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:9920000-9925600	Weak transcription	NH-A	brain
47	chr1:9920000-9929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:9920000-9929400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:9920000-9929600	Weak transcription	Thymus	Thymus
50	chr1:9920000-9930400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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