Variant report

Variant	rs11941546
Chromosome Location	chr4:148838641-148838642
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10519921	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11930900	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11934409	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11937178	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11939997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11942547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11946732	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13434578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13435747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17024137	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17024143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024182	1.00[CEU][hapmap]
rs187006	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2118033	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2118035	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2164530	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2358180	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2358181	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2575585	1.00[CEU][hapmap]
rs2635256	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2635266	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2635267	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2635268	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4027114	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4027115	0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4337713	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55752555	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67913037	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72617450	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72959726	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7666206	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7669783	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs7672161	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7685779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs975371	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs975372	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024596	chr4:148830472-148886915	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
2	chr4:148796800-148863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
4	chr4:148797400-148879600	Weak transcription	Gastric	stomach
5	chr4:148804600-148854400	Weak transcription	Psoas Muscle	Psoas
6	chr4:148820600-148861200	Weak transcription	Esophagus	oesophagus
7	chr4:148820800-148848800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:148824400-148842800	Weak transcription	Lung	lung
9	chr4:148824400-148854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:148824600-148854400	Weak transcription	Right Ventricle	heart
11	chr4:148825200-148839600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:148825200-148847400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr4:148825200-148848400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:148825400-148843400	Weak transcription	Fetal Heart	heart
15	chr4:148825400-148844200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:148825400-148846200	Weak transcription	Fetal Kidney	kidney
17	chr4:148825400-148861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
19	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
20	chr4:148827400-148861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:148829400-148864200	Weak transcription	Primary T cells from cord blood	blood
22	chr4:148830200-148841200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:148830600-148840200	Weak transcription	Spleen	Spleen
24	chr4:148830800-148845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:148831400-148842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:148831600-148849000	Weak transcription	NH-A	brain
27	chr4:148832000-148839000	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:148832200-148848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:148832200-148854400	Weak transcription	NHEK	skin
30	chr4:148832600-148845600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:148833600-148848400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:148833600-148877400	Weak transcription	Small Intestine	intestine
33	chr4:148834200-148845200	Strong transcription	HSMM	muscle
34	chr4:148834800-148849000	Weak transcription	NHLF	lung
35	chr4:148834800-148861400	Weak transcription	Fetal Intestine Large	intestine
36	chr4:148835000-148867200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:148835000-148869000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:148835600-148848800	Weak transcription	Fetal Stomach	stomach
39	chr4:148835600-148854400	Weak transcription	Fetal Intestine Small	intestine
40	chr4:148836400-148843000	Weak transcription	Aorta	Aorta
41	chr4:148836400-148848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:148836400-148861000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:148836600-148842600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:148836600-148867000	Weak transcription	HMEC	breast
45	chr4:148836800-148842800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:148837400-148838800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:148837600-148838800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:148837600-148838800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:148837600-148839200	Strong transcription	GM12878-XiMat	blood
50	chr4:148837600-148850600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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