Variant report

Variant	rs10774198
Chromosome Location	chr12:4258438-4258439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10459129	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10744631	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10774197	0.84[MEX][hapmap];0.82[YRI][hapmap]
rs10848986	0.91[EUR][1000 genomes]
rs10848988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10848989	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11063011	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11063012	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11063013	0.89[EUR][1000 genomes]
rs1861175	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1978311	0.94[EUR][1000 genomes]
rs6489518	0.82[ASN][1000 genomes]
rs6489519	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7137733	0.98[EUR][1000 genomes]
rs7298575	0.82[ASN][1000 genomes]
rs7298905	0.88[EUR][1000 genomes]
rs7304518	0.98[EUR][1000 genomes]
rs759310	0.83[AMR][1000 genomes];0.94[EUR][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10774198	CD4	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4252400-4262600	Weak transcription	Esophagus	oesophagus
2	chr12:4252400-4262600	Weak transcription	Lung	lung
3	chr12:4254600-4259400	Enhancers	Primary B cells from cord blood	blood
4	chr12:4254800-4264400	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:4255200-4258600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:4256800-4258600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:4256800-4261000	Weak transcription	K562	blood
8	chr12:4256800-4265400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:4257000-4262800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:4257000-4265400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:4257200-4260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:4257200-4265400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:4257800-4261000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:4257800-4261000	Weak transcription	Fetal Thymus	thymus
15	chr12:4258000-4260800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:4258000-4261000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:4258000-4261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:4258000-4261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:4258000-4262000	Weak transcription	Spleen	Spleen
20	chr12:4258000-4262600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:4258000-4262600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:4258000-4262600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:4258000-4262600	Weak transcription	Stomach Mucosa	stomach
24	chr12:4258000-4262600	Weak transcription	NHEK	skin
25	chr12:4258000-4262800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:4258200-4261000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:4258200-4261000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:4258200-4261200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:4258200-4261200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:4258200-4261200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:4258200-4261200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:4258200-4261600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:4258200-4261800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:4258200-4262600	Weak transcription	Colonic Mucosa	Colon
35	chr12:4258200-4262600	Weak transcription	Small Intestine	intestine
36	chr12:4258200-4262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:4258400-4260600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:4258400-4260800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:4258400-4260800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:4258400-4260800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:4258400-4260800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:4258400-4260800	Enhancers	GM12878-XiMat	blood
43	chr12:4258400-4261000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:4258400-4261000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:4258400-4261000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:4258400-4265200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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