Variant report

Variant	rs10185455
Chromosome Location	chr2:153488963-153488964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153031601..153033493-chr2:153487450..153489927,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10178618	0.90[CHD][hapmap];0.80[LWK][hapmap];0.83[ASN][1000 genomes]
rs11679491	0.81[ASN][1000 genomes]
rs11883762	0.90[CHD][hapmap];0.80[LWK][hapmap];0.85[ASN][1000 genomes]
rs11899051	0.85[YRI][hapmap]
rs13018870	0.83[ASN][1000 genomes]
rs13419068	0.84[YRI][hapmap]
rs1561267	0.90[CHD][hapmap];0.80[LWK][hapmap];0.85[ASN][1000 genomes]
rs16831451	0.85[CHD][hapmap]
rs16831529	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs16831728	0.90[CHD][hapmap]
rs1962313	0.81[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs1965785	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272535	0.83[ASN][1000 genomes]
rs2346539	0.85[YRI][hapmap]
rs3748938	0.80[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs3748941	0.83[ASN][1000 genomes]
rs3811570	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.87[ASN][1000 genomes]
rs3817620	0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs4146903	0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs4267470	0.85[YRI][hapmap]
rs4664119	0.83[ASN][1000 genomes]
rs4664121	0.85[YRI][hapmap]
rs6434129	0.91[ASN][1000 genomes]
rs6710417	0.85[ASN][1000 genomes]
rs6714218	0.83[ASN][1000 genomes]
rs746780	0.84[ASN][1000 genomes]
rs7556673	0.82[ASW][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.84[YRI][hapmap]
rs7582253	0.89[YRI][hapmap]
rs7592127	0.83[ASN][1000 genomes]
rs7604573	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs893328	0.85[ASN][1000 genomes]

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	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693437	chr2:153484685-153505003	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10185455	PRPF40A	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153454800-153496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:153457200-153505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:153463800-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:153464000-153502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:153467200-153504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:153468600-153495800	Weak transcription	Esophagus	oesophagus
7	chr2:153468800-153492000	Weak transcription	Liver	Liver
8	chr2:153469000-153493800	Weak transcription	Spleen	Spleen
9	chr2:153469000-153496400	Weak transcription	Colonic Mucosa	Colon
10	chr2:153469000-153509800	Weak transcription	Small Intestine	intestine
11	chr2:153469200-153495200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:153469600-153496800	Weak transcription	HSMM	muscle
13	chr2:153471000-153507000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:153473000-153500600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:153473800-153496400	Weak transcription	Osteobl	bone
17	chr2:153474400-153505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:153475800-153493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:153476600-153492800	Weak transcription	Gastric	stomach
20	chr2:153477600-153489800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:153477800-153493800	Weak transcription	HSMMtube	muscle
22	chr2:153477800-153496000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:153477800-153496600	Weak transcription	Aorta	Aorta
24	chr2:153479400-153496200	Weak transcription	NH-A	brain
25	chr2:153481000-153490200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:153481200-153491200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:153481200-153493400	Weak transcription	Fetal Brain Male	brain
28	chr2:153481200-153502200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:153481200-153502400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:153481400-153490400	Strong transcription	NHEK	skin
31	chr2:153481400-153502400	Strong transcription	Placenta	Placenta
32	chr2:153481400-153503000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:153481600-153489400	Strong transcription	HMEC	breast
34	chr2:153482000-153490600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:153482000-153493600	Weak transcription	NHLF	lung
36	chr2:153483000-153491200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:153483800-153494400	Weak transcription	NHDF-Ad	bronchial
38	chr2:153484200-153490600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:153484200-153490600	Strong transcription	Brain Substantia Nigra	brain
40	chr2:153484400-153490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:153484400-153490600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:153484400-153491200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:153484400-153491800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr2:153484400-153492000	Strong transcription	Brain Hippocampus Middle	brain
45	chr2:153484400-153492200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:153484400-153496000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:153484400-153502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:153484400-153503000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:153484400-153504200	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:153484600-153490600	Strong transcription	Adipose Nuclei	Adipose

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