Variant report

Variant	rs10746004
Chromosome Location	chr12:105001822-105001823
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104995476..104999568-chr12:105000294..105003603,4	MCF-7	breast:
2	chr12:105001524..105004120-chr12:105024508..105026031,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10778342	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2162661	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2888827	0.94[EUR][1000 genomes]
rs3812796	0.94[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6539162	0.88[EUR][1000 genomes]
rs6539163	1.00[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6539164	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7316145	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7972130	0.94[EUR][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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10746004	CRY1	cis	parietal	SCAN
rs10746004	UTP20	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104989400-105030600	Strong transcription	Dnd41	blood
2	chr12:104993200-105006200	Weak transcription	Fetal Heart	heart
3	chr12:104993200-105012600	Weak transcription	Gastric	stomach
4	chr12:104996800-105002600	Weak transcription	Fetal Brain Female	brain
5	chr12:104997200-105003800	Weak transcription	Fetal Brain Male	brain
6	chr12:104997200-105004600	Enhancers	Placenta	Placenta
7	chr12:104997800-105002200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:104998000-105002600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:104998000-105004400	Weak transcription	Stomach Mucosa	stomach
10	chr12:104998000-105008600	Weak transcription	Right Ventricle	heart
11	chr12:104998200-105003200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:104998200-105008400	Weak transcription	Esophagus	oesophagus
13	chr12:104998400-105002400	Weak transcription	Brain Anterior Caudate	brain
14	chr12:104998400-105002600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:104998400-105002800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:104998400-105003400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:104998400-105005000	Weak transcription	Spleen	Spleen
18	chr12:104998400-105008400	Weak transcription	Aorta	Aorta
19	chr12:104998400-105008400	Weak transcription	Right Atrium	heart
20	chr12:104998400-105008600	Weak transcription	Small Intestine	intestine
21	chr12:104998600-105002400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:104998600-105003200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:104998600-105003200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:104998600-105003800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:104998600-105005200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:104998600-105008600	Weak transcription	Primary T cells from cord blood	blood
27	chr12:104998600-105012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:104998800-105002600	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:104998800-105031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:104999000-105005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:104999000-105026800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:104999600-105003600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:104999600-105004000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:104999800-105002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:104999800-105002600	Weak transcription	K562	blood
36	chr12:104999800-105004200	Weak transcription	GM12878-XiMat	blood
37	chr12:104999800-105005200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:104999800-105005400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:104999800-105005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:104999800-105008800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:104999800-105012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:105000000-105002800	Weak transcription	Brain Germinal Matrix	brain
43	chr12:105000000-105004600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:105000000-105005400	Weak transcription	Primary B cells from cord blood	blood
45	chr12:105000000-105020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:105000000-105021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:105000200-105002000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:105000200-105004800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:105000200-105008400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:105000400-105002800	Weak transcription	NHEK	skin

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