Variant report

Variant	rs2271004
Chromosome Location	chr1:58996203-58996204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11207241	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12131820	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139614	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587822	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs697592	0.82[CHB][hapmap];0.83[MEX][hapmap]
rs697594	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs697595	0.82[AMR][1000 genomes];0.84[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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv998092	chr1:58978327-59002319	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2271004	KANK4	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:58953600-58999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:58963800-58999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
5	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:58974800-59005000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:58974800-59010800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
9	chr1:58975000-59010600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:58975000-59010800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:58977200-59005000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:58977200-59010800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:58977200-59011400	Weak transcription	Ovary	ovary
14	chr1:58977400-58999000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:58977400-59005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:58977400-59008600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:58977400-59010400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:58977400-59010600	Weak transcription	Aorta	Aorta
19	chr1:58977400-59010600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:58977400-59010600	Weak transcription	Psoas Muscle	Psoas
21	chr1:58977400-59011400	Weak transcription	Left Ventricle	heart
22	chr1:58977400-59011400	Weak transcription	Lung	lung
23	chr1:58977600-59011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:58978200-59010200	Weak transcription	Dnd41	blood
25	chr1:58979000-59005400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:58979000-59011400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:58980400-58997600	Weak transcription	GM12878-XiMat	blood
28	chr1:58982200-59008200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:58982800-58998000	Weak transcription	HSMMtube	muscle
30	chr1:58984400-58996400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:58985200-59010600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:58985800-59010400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:58985800-59010600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:58989000-58998800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:58989200-59004600	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:58989200-59010600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:58989400-59010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:58989800-58997400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:58990800-59008200	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:58990800-59011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:58991400-59003800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:58991600-58999600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:58992400-59003400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:58992400-59010800	Weak transcription	Adipose Nuclei	Adipose
45	chr1:58993000-58997200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:58993000-58997400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:58993000-59001800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:58993000-59002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:58993000-59004400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:58993000-59008400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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