Variant report

Variant	rs10199661
Chromosome Location	chr2:149013268-149013269
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084286	1.00[AMR][1000 genomes]
rs10168627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10169814	1.00[AMR][1000 genomes]
rs10172107	0.89[AFR][1000 genomes]
rs10172459	0.89[AFR][1000 genomes]
rs10172623	1.00[AMR][1000 genomes]
rs10172638	1.00[AMR][1000 genomes]
rs10174213	1.00[AMR][1000 genomes]
rs10174231	1.00[AMR][1000 genomes]
rs10174899	0.89[AFR][1000 genomes]
rs10175126	0.89[AFR][1000 genomes]
rs10179991	0.89[AFR][1000 genomes]
rs10180813	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181462	0.89[AFR][1000 genomes]
rs10186976	0.89[AFR][1000 genomes]
rs10187257	0.89[AFR][1000 genomes]
rs10189852	0.89[AFR][1000 genomes]
rs10191867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10195846	1.00[AMR][1000 genomes]
rs10197288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10199100	0.89[AFR][1000 genomes]
rs10206286	0.89[AFR][1000 genomes]
rs10211580	1.00[AMR][1000 genomes]
rs13385606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385697	0.89[AFR][1000 genomes]
rs13386143	1.00[AMR][1000 genomes]
rs13387197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13395948	1.00[AMR][1000 genomes]
rs13396012	1.00[AMR][1000 genomes]
rs13397712	0.89[AFR][1000 genomes]
rs13399551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401666	1.00[AMR][1000 genomes]
rs13403934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404496	1.00[AMR][1000 genomes]
rs13404809	1.00[AMR][1000 genomes]
rs13417167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13420788	0.89[AFR][1000 genomes]
rs13422826	0.89[AFR][1000 genomes]
rs13426081	0.89[AFR][1000 genomes]
rs13426527	1.00[AMR][1000 genomes]
rs28405957	0.89[AFR][1000 genomes]
rs28594070	0.89[AFR][1000 genomes]
rs28647742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148994800-149016600	Weak transcription	Fetal Brain Male	brain
2	chr2:148995000-149019800	Weak transcription	Aorta	Aorta
3	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
4	chr2:148995400-149013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:148995400-149015200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:148999400-149016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:149002600-149015600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:149002800-149016600	Weak transcription	NHLF	lung
10	chr2:149008000-149013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:149009200-149016600	ZNF genes & repeats	GM12878-XiMat	blood
12	chr2:149009400-149017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:149009600-149017600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr2:149010400-149013600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:149010800-149013400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:149010800-149013400	Weak transcription	HSMM	muscle
17	chr2:149010800-149014800	ZNF genes & repeats	Dnd41	blood
18	chr2:149011000-149013600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr2:149011000-149014400	ZNF genes & repeats	Fetal Stomach	stomach
20	chr2:149011000-149017000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:149011200-149013600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr2:149011200-149014200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
23	chr2:149011200-149014400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:149011400-149013800	ZNF genes & repeats	Fetal Brain Female	brain
25	chr2:149011400-149014000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:149011400-149014000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr2:149011400-149014000	ZNF genes & repeats	Spleen	Spleen
28	chr2:149011400-149016400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:149011600-149013600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
30	chr2:149011600-149014200	ZNF genes & repeats	Thymus	Thymus
31	chr2:149011600-149014400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr2:149011600-149017000	Strong transcription	Fetal Intestine Large	intestine
33	chr2:149011600-149017200	ZNF genes & repeats	Fetal Thymus	thymus
34	chr2:149011600-149017600	ZNF genes & repeats	Fetal Muscle Leg	muscle
35	chr2:149011600-149030800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:149011800-149013400	Weak transcription	HSMMtube	muscle
37	chr2:149011800-149013600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:149011800-149014600	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr2:149011800-149015400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:149011800-149016400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:149011800-149016600	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:149011800-149016800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:149011800-149021200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:149012000-149017000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:149012000-149017000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:149012000-149019000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:149012200-149013800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:149012200-149014000	Strong transcription	Fetal Lung	lung
49	chr2:149012200-149015800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:149012200-149016600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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