Variant report

Variant	rs10844187
Chromosome Location	chr12:32486059-32486060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1058640	0.83[YRI][hapmap]
rs10771939	0.86[JPT][hapmap]
rs10771940	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs10844189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10844193	0.83[YRI][hapmap]
rs10844194	0.89[CEU][hapmap]
rs11051966	0.89[CEU][hapmap]
rs11051967	0.85[CEU][hapmap]
rs12312730	0.86[JPT][hapmap]
rs16919768	0.86[JPT][hapmap]
rs2291419	0.86[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs261900	0.88[JPT][hapmap]
rs3789976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955481	0.86[JPT][hapmap]
rs901600	0.85[JPT][hapmap]
rs904639	0.86[JPT][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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10844187	BICD1	Cis_1M	lymphoblastoid	RTeQTL
rs10844187	OVCH1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32449600-32490200	Weak transcription	HSMMtube	muscle
2	chr12:32457200-32494400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:32460400-32514600	Weak transcription	HMEC	breast
4	chr12:32472600-32489200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:32472800-32493600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:32475000-32490200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:32475400-32500200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:32475600-32532400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:32475800-32492000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:32475800-32495800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:32475800-32502200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:32475800-32512200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:32476400-32505600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:32476400-32515400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:32476600-32487200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:32476600-32493400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:32477200-32490400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:32477200-32500800	Weak transcription	Hela-S3	cervix
19	chr12:32478400-32490400	Weak transcription	NHLF	lung
20	chr12:32478600-32490200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:32478600-32490400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:32478800-32490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:32478800-32490400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:32478800-32498800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:32479000-32493600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:32479200-32492400	Weak transcription	Small Intestine	intestine
27	chr12:32479200-32502200	Weak transcription	NHDF-Ad	bronchial
28	chr12:32479200-32504200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:32479400-32490400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:32479400-32494400	Weak transcription	Right Ventricle	heart
31	chr12:32479400-32501200	Weak transcription	Fetal Brain Male	brain
32	chr12:32479600-32491800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:32480200-32494000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:32480600-32524800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:32481000-32487000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:32481000-32490400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:32481200-32490400	Weak transcription	NH-A	brain
38	chr12:32481200-32493800	Weak transcription	Fetal Thymus	thymus
39	chr12:32481400-32490400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:32481400-32511800	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:32481600-32486200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:32481600-32490400	Weak transcription	Primary B cells from cord blood	blood
43	chr12:32481600-32490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:32481600-32490400	Weak transcription	Brain Angular Gyrus	brain
45	chr12:32481600-32490400	Weak transcription	Fetal Intestine Large	intestine
46	chr12:32481600-32490400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:32481600-32490600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:32481600-32496600	Weak transcription	Brain Anterior Caudate	brain
49	chr12:32481600-32497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:32481600-32501800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links