Variant report

Variant	rs41312643
Chromosome Location	chr1:78325622-78325623
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2018593	0.87[EUR][1000 genomes]
rs41313399	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6604877	0.87[EUR][1000 genomes]
rs6662245	0.87[AMR][1000 genomes]
rs6666107	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6677011	0.87[AMR][1000 genomes]
rs6679645	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6701361	0.87[EUR][1000 genomes]
rs74092331	0.90[EUR][1000 genomes]
rs7523258	0.87[EUR][1000 genomes]
rs7532455	0.87[AMR][1000 genomes]
rs7548467	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7549028	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7550587	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7555421	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7555864	0.87[AMR][1000 genomes]
rs9659817	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9661421	0.93[EUR][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv947433	chr1:78310844-78325736	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:78284600-78333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:78285600-78332000	Weak transcription	Spleen	Spleen
4	chr1:78286400-78333200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:78286600-78328400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:78290200-78334200	Weak transcription	Gastric	stomach
7	chr1:78296800-78329000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:78298400-78340400	Weak transcription	Colonic Mucosa	Colon
9	chr1:78298600-78327000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
11	chr1:78298800-78332800	Weak transcription	Fetal Kidney	kidney
12	chr1:78299400-78340200	Weak transcription	NHEK	skin
13	chr1:78299400-78341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:78299600-78340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:78299600-78343000	Weak transcription	K562	blood
16	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:78300200-78331600	Weak transcription	Lung	lung
18	chr1:78300200-78332600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:78300800-78328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:78300800-78342200	Weak transcription	Fetal Brain Male	brain
21	chr1:78301400-78332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
23	chr1:78301800-78342400	Weak transcription	NHLF	lung
24	chr1:78302000-78332000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:78302800-78334200	Weak transcription	HepG2	liver
26	chr1:78303800-78326000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:78303800-78332800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:78305800-78332200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:78305800-78342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:78306000-78342600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:78309200-78328800	Weak transcription	NH-A	brain
32	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
33	chr1:78309400-78326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:78309600-78330200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:78309800-78328000	Weak transcription	Placenta	Placenta
36	chr1:78310400-78332000	Weak transcription	Fetal Thymus	thymus
37	chr1:78310600-78331600	Weak transcription	Left Ventricle	heart
38	chr1:78310800-78327000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:78310800-78333000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:78311000-78332600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:78312000-78332800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:78312000-78353000	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:78313000-78328800	Weak transcription	GM12878-XiMat	blood
44	chr1:78313000-78331800	Weak transcription	Osteobl	bone
45	chr1:78313000-78353200	Weak transcription	HUVEC	blood vessel
46	chr1:78313200-78325800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:78313400-78329000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:78313400-78329000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:78313400-78343200	Weak transcription	Pancreas	Pancrea
50	chr1:78313800-78330400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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