Variant report

Variant	rs10840648
Chromosome Location	chr12:122084847-122084848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122084038..122086515-chr12:122089588..122092191,2	K562	blood:
2	chr12:122064452..122066537-chr12:122084416..122086482,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182500	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10770183	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840650	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043296	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043306	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11043308	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11614109	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12305333	0.82[EUR][1000 genomes]
rs12313273	0.83[MEX][hapmap]
rs12315280	0.83[ASN][1000 genomes]
rs12322922	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1983269	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594507	0.84[ASW][hapmap];0.83[CHD][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs28637676	0.91[CEU][hapmap]
rs3741595	0.84[ASW][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs6486795	0.83[MEX][hapmap]
rs7313601	0.83[MEX][hapmap]
rs7484839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7485243	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7487117	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10840648	KCNC2	trans	parietal	SCAN
rs10840648	NME2P1	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122066200-122090400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:122066400-122096600	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122067800-122096600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:122069400-122090800	Weak transcription	Hela-S3	cervix
5	chr12:122071200-122087200	Weak transcription	Left Ventricle	heart
6	chr12:122071400-122088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:122071400-122090200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:122071400-122095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:122071400-122096600	Weak transcription	Colonic Mucosa	Colon
10	chr12:122071400-122096600	Weak transcription	Right Atrium	heart
11	chr12:122073000-122089400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:122073000-122091200	Strong transcription	Fetal Intestine Small	intestine
13	chr12:122073200-122085600	Weak transcription	HSMMtube	muscle
14	chr12:122076200-122091200	Strong transcription	Fetal Stomach	stomach
15	chr12:122076400-122090600	Weak transcription	NHEK	skin
16	chr12:122076800-122086400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:122076800-122087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:122077400-122085200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:122077400-122096400	Weak transcription	Osteobl	bone
20	chr12:122078800-122086400	Strong transcription	Primary T cells from cord blood	blood
21	chr12:122079200-122087200	Weak transcription	K562	blood
22	chr12:122079200-122093600	Weak transcription	Fetal Brain Female	brain
23	chr12:122079400-122096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:122079600-122089400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:122079600-122096600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:122079800-122089400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:122079800-122091000	Weak transcription	Small Intestine	intestine
28	chr12:122080000-122086400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:122080000-122087200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:122080000-122089200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:122080000-122090600	Weak transcription	Esophagus	oesophagus
32	chr12:122080000-122090800	Weak transcription	Right Ventricle	heart
33	chr12:122080000-122092800	Weak transcription	NHLF	lung
34	chr12:122080000-122096600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:122080000-122096600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:122080000-122096600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:122080000-122096600	Weak transcription	Fetal Intestine Large	intestine
38	chr12:122080000-122096600	Weak transcription	Gastric	stomach
39	chr12:122080200-122086400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:122080200-122086800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:122080200-122088000	Weak transcription	Placenta	Placenta
42	chr12:122080200-122089600	Weak transcription	Liver	Liver
43	chr12:122080200-122090400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:122080200-122090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:122080200-122090800	Weak transcription	Pancreas	Pancrea
46	chr12:122080200-122091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:122080200-122096400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:122080200-122096600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:122080200-122096600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:122080200-122096800	Weak transcription	Stomach Smooth Muscle	stomach

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