Variant report

Variant	rs2244935
Chromosome Location	chr1:212900487-212900488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212891784..212893454-chr1:212900390..212902771,2	MCF-7	breast:
2	chr1:212899078..212902510-chr1:212913251..212915180,3	K562	blood:
3	chr1:212899078..212902712-chr1:212913429..212916281,3	K562	blood:
4	chr1:212900071..212902059-chr1:212903736..212906563,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10864008	0.81[ASN][1000 genomes]
rs1284800	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs1298196	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1770777	1.00[CEU][hapmap]
rs1770778	1.00[CEU][hapmap]
rs2359321	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2456814	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2456815	1.00[ASW][hapmap]
rs2492783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2492786	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2492787	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501836	0.93[ASN][1000 genomes]
rs2501837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501838	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2792558	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs3006239	0.88[AFR][1000 genomes]
rs3006242	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58172415	0.81[ASN][1000 genomes]
rs6677411	0.92[CHB][hapmap]
rs73083789	0.84[ASN][1000 genomes]
rs7528113	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2244935	C1orf227	cis	lymphoblastoid	seeQTL
rs2244935	NSL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895200-212922800	Weak transcription	Left Ventricle	heart
2	chr1:212895400-212901800	Weak transcription	Liver	Liver
3	chr1:212895400-212902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:212895400-212902400	Weak transcription	Primary T cells from cord blood	blood
5	chr1:212895400-212906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:212895400-212906600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:212895400-212912000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:212895400-212914600	Weak transcription	Spleen	Spleen
9	chr1:212895400-212916600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:212895400-212917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:212895400-212923200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:212895400-212923400	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:212895400-212923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
15	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
16	chr1:212895600-212900600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:212895600-212900600	Weak transcription	NH-A	brain
18	chr1:212895600-212901000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:212895600-212904000	Weak transcription	GM12878-XiMat	blood
20	chr1:212895600-212905600	Weak transcription	Lung	lung
21	chr1:212895600-212923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:212895600-212923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:212895600-212964600	Weak transcription	Gastric	stomach
24	chr1:212895800-212900600	Weak transcription	NHDF-Ad	bronchial
25	chr1:212895800-212901400	Weak transcription	Stomach Mucosa	stomach
26	chr1:212895800-212911200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:212895800-212917400	Weak transcription	NHLF	lung
28	chr1:212895800-212925600	Weak transcription	Small Intestine	intestine
29	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
30	chr1:212896000-212900800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:212896000-212911800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:212896000-212917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:212896200-212901400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:212896200-212902200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:212896200-212906000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:212896200-212908200	Weak transcription	K562	blood
37	chr1:212896200-212912200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:212896400-212906000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:212896400-212917000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:212896800-212909000	Weak transcription	Primary B cells from cord blood	blood
41	chr1:212897200-212900600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:212897400-212914600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:212897800-212911600	Weak transcription	Brain Germinal Matrix	brain
44	chr1:212898400-212909600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:212898600-212903800	Weak transcription	Adipose Nuclei	Adipose
46	chr1:212898600-212923200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:212898800-212902400	Weak transcription	Fetal Lung	lung
48	chr1:212898800-212911800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:212899200-212901800	Enhancers	HepG2	liver

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