Variant report

Variant	rs7954976
Chromosome Location	chr12:51681903-51681904
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	chr12:51679852..51682004-chr12:51687950..51689517,2	K562	blood:
2	chr12:51418715..51421424-chr12:51679999..51682446,2	K562	blood:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10876156	0.87[CEU][hapmap]
rs1130641	0.81[CEU][hapmap]
rs11341	0.86[CEU][hapmap]
rs12227330	0.83[LWK][hapmap]
rs1362963	0.82[ASW][hapmap];0.93[LWK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs17860299	0.92[TSI][hapmap]
rs17860317	0.86[TSI][hapmap]
rs1965075	0.80[AFR][1000 genomes]
rs1991433	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114876	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288367	0.93[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2359450	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3210837	0.82[ASW][hapmap];0.90[LWK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs3847855	0.87[ASW][hapmap];0.85[LWK][hapmap]
rs3858637	0.86[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3969069	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4409892	0.84[AFR][1000 genomes]
rs4477479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4761994	0.99[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4762011	0.86[AFR][1000 genomes]
rs4762012	0.83[AFR][1000 genomes]
rs6580821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133314	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135343	0.86[AFR][1000 genomes]
rs7135736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135840	0.86[AFR][1000 genomes]
rs7306505	0.86[AFR][1000 genomes]
rs7306875	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7308177	0.81[EUR][1000 genomes]
rs7311196	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7312857	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs7316221	0.81[EUR][1000 genomes]
rs7316433	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs7316604	0.81[EUR][1000 genomes]
rs74093810	0.81[EUR][1000 genomes]
rs74093814	0.81[EUR][1000 genomes]
rs7957868	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7975715	0.81[EUR][1000 genomes]
rs9795598	0.81[AFR][1000 genomes]
rs9795976	0.93[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7954976	MFSD5	cis	parietal	SCAN
rs7954976	COL2A1	cis	parietal	SCAN
rs7954976	FAM186B	cis	parietal	SCAN
rs7954976	ZNF641	cis	cerebellum	SCAN
rs7954976	KCNH3	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51664600-51683200	Weak transcription	Spleen	Spleen
2	chr12:51664600-51692800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:51664800-51685800	Weak transcription	Esophagus	oesophagus
4	chr12:51673200-51685200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:51673400-51684800	Weak transcription	GM12878-XiMat	blood
6	chr12:51673800-51685400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:51673800-51697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:51674000-51683400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:51674000-51698400	Strong transcription	Fetal Thymus	thymus
10	chr12:51674000-51701400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:51674200-51685400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:51674200-51685600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:51674400-51685200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:51674400-51698400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:51674400-51698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:51674400-51698800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:51674400-51700600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:51674600-51685800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:51674600-51686000	Strong transcription	Primary T cells from cord blood	blood
21	chr12:51675200-51685600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:51676600-51685800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:51676800-51691000	Weak transcription	Placenta	Placenta
24	chr12:51678000-51697600	Weak transcription	Adipose Nuclei	Adipose
25	chr12:51678800-51693000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:51679200-51685000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:51679800-51685600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr12:51679800-51686800	Strong transcription	Thymus	Thymus
29	chr12:51680000-51682000	Weak transcription	Primary B cells from cord blood	blood
30	chr12:51680000-51687600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:51680600-51701600	Weak transcription	Small Intestine	intestine
32	chr12:51681200-51682800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:51681200-51696600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:51681800-51684200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:51681800-51684200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:51681800-51688000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:51681800-51714200	Weak transcription	Gastric	stomach

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