Variant report

Variant	rs7954140
Chromosome Location	chr12:51490408-51490409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51475858..51478802-chr12:51488243..51491629,4	K562	blood:
2	chr12:51474025..51479149-chr12:51485745..51494502,15	MCF-7	breast:
3	chr12:51480017..51482806-chr12:51490046..51492901,2	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1005559	0.85[EUR][1000 genomes]
rs1048230	0.81[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs10506298	0.82[EUR][1000 genomes]
rs10506299	0.82[EUR][1000 genomes]
rs1056897	0.94[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs10747604	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169633	0.80[EUR][1000 genomes]
rs11169636	0.80[EUR][1000 genomes]
rs11169637	0.80[EUR][1000 genomes]
rs11169641	0.80[EUR][1000 genomes]
rs11169642	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11169644	0.80[EUR][1000 genomes]
rs11169647	0.80[EUR][1000 genomes]
rs11169648	0.80[EUR][1000 genomes]
rs11169649	0.80[EUR][1000 genomes]
rs11169652	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11169654	0.81[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169655	0.82[EUR][1000 genomes]
rs11169661	0.82[EUR][1000 genomes]
rs11169667	0.82[EUR][1000 genomes]
rs11169669	0.82[EUR][1000 genomes]
rs11169670	0.82[EUR][1000 genomes]
rs11169671	0.82[EUR][1000 genomes]
rs11169672	0.81[EUR][1000 genomes]
rs11169682	0.93[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes]
rs11169712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169731	0.93[JPT][hapmap]
rs11169752	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs11519977	0.80[EUR][1000 genomes]
rs11738	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs11831810	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11831946	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11833022	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11834746	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12366476	0.80[EUR][1000 genomes]
rs12366756	0.82[EUR][1000 genomes]
rs12369639	0.82[CEU][hapmap]
rs12370820	0.97[EUR][1000 genomes]
rs12371463	0.83[EUR][1000 genomes]
rs12372173	0.85[EUR][1000 genomes]
rs12809563	0.80[EUR][1000 genomes]
rs12809790	0.89[ASN][1000 genomes]
rs12810174	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12810596	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810659	0.82[EUR][1000 genomes]
rs12810700	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810990	0.89[ASN][1000 genomes]
rs12811508	0.87[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12811658	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12811684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812650	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12813309	0.96[EUR][1000 genomes]
rs12813368	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813728	0.81[EUR][1000 genomes]
rs12814498	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12817386	0.82[EUR][1000 genomes]
rs12818033	0.80[EUR][1000 genomes]
rs12819225	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12819517	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12820074	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12820559	0.81[JPT][hapmap]
rs12820966	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821444	0.80[EUR][1000 genomes]
rs12822509	0.98[EUR][1000 genomes]
rs12823402	0.85[EUR][1000 genomes]
rs12824225	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12824958	0.81[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs12826153	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12827861	0.82[EUR][1000 genomes]
rs12828349	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828536	0.85[EUR][1000 genomes]
rs12829630	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12830048	0.80[EUR][1000 genomes]
rs12830073	0.85[EUR][1000 genomes]
rs12831269	0.82[EUR][1000 genomes]
rs12833565	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs15897	0.82[EUR][1000 genomes]
rs17125137	0.81[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs17296192	0.87[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2285228	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2285230	0.81[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2301529	0.81[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs34057357	0.83[EUR][1000 genomes]
rs34481246	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34498074	0.85[AMR][1000 genomes]
rs34735738	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35037088	0.80[EUR][1000 genomes]
rs4768964	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768967	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580792	0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580793	0.87[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67133203	0.84[EUR][1000 genomes]
rs67259551	0.82[EUR][1000 genomes]
rs67260912	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67293043	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7135059	0.97[EUR][1000 genomes]
rs71445772	0.80[EUR][1000 genomes]
rs7305638	0.80[EUR][1000 genomes]
rs7306293	0.80[EUR][1000 genomes]
rs7959075	0.80[EUR][1000 genomes]
rs7959082	0.80[EUR][1000 genomes]
rs7960381	0.81[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs7964570	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972406	0.85[EUR][1000 genomes]
rs7975147	0.85[EUR][1000 genomes]
rs7976777	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7977104	0.94[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs7978723	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7980874	0.97[EUR][1000 genomes]
rs970098	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs970099	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7954140	TFCP2	cis	cerebellum	SCAN
rs7954140	TMPRSS12	cis	parietal	SCAN
rs7954140	KRT79	cis	cerebellum	SCAN
rs7954140	SCN8A	cis	cerebellum	SCAN
rs7954140	DDN	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51492600	Weak transcription	Esophagus	oesophagus
3	chr12:51477800-51499600	Weak transcription	NHLF	lung
4	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
6	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:51478000-51496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:51478200-51493200	Weak transcription	Fetal Brain Male	brain
9	chr12:51479800-51492000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
12	chr12:51483000-51492200	Weak transcription	K562	blood
13	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:51484000-51491000	Strong transcription	HSMM	muscle
15	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:51485200-51493400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
25	chr12:51485800-51497400	Strong transcription	Fetal Intestine Small	intestine
26	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:51486000-51490600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:51486000-51490800	Strong transcription	GM12878-XiMat	blood
29	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:51487000-51490800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:51487200-51498000	Strong transcription	Osteobl	bone
41	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:51487400-51490800	Strong transcription	A549	lung
49	chr12:51487400-51496400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:51487400-51498200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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