Variant report

Variant	rs41302796
Chromosome Location	chr1:84969565-84969566
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:84969497-84969805	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
3	WRNIP1	chr1:84969310-84969754	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:84969417-84969617	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:84968320-84972670	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:84969408-84972646	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:84968524-84972839	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:84969362-84973189	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:84968683-84972955	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:84969345-84972778	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr1:84968805-84973213	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:84969317-84972923	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:84969488-84969887	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
2	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
3	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
SPATA1	TF binding region
GNG5	TF binding region
ENSG00000271576	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1395418	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17365681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17365723	1.00[EUR][1000 genomes]
rs17374048	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17374753	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17540101	0.96[EUR][1000 genomes]
rs312403	1.00[EUR][1000 genomes]
rs41284589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41284591	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41284599	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41293029	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4512665	1.00[EUR][1000 genomes]
rs4907081	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72946368	0.94[EUR][1000 genomes]
rs72946369	0.96[EUR][1000 genomes]
rs72946390	0.96[EUR][1000 genomes]
rs72948408	0.96[EUR][1000 genomes]
rs72948421	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72948483	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
2	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
5	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:84956800-84970400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:84958600-84970400	Weak transcription	Lung	lung
8	chr1:84963000-84969600	Weak transcription	Colonic Mucosa	Colon
9	chr1:84963800-84970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:84963800-84970200	Weak transcription	Fetal Brain Male	brain
11	chr1:84963800-84970400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:84964000-84969800	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:84964000-84969800	Weak transcription	Ovary	ovary
14	chr1:84964000-84970200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:84964600-84969600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:84965800-84970400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:84966000-84969600	Weak transcription	Thymus	Thymus
18	chr1:84966800-84970400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:84967000-84969600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:84967000-84970000	Weak transcription	Placenta	Placenta
21	chr1:84967400-84969600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:84967400-84970200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:84967400-84970600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:84967600-84970600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:84967800-84970600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr1:84968000-84969600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:84968200-84969600	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:84968200-84969600	Enhancers	Fetal Intestine Small	intestine
29	chr1:84968200-84970000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:84968200-84970000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:84968200-84970200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:84968200-84970600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:84968200-84970600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:84968400-84969800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:84968400-84970400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:84968600-84969600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:84968600-84969600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:84968600-84969800	Enhancers	Primary B cells from cord blood	blood
39	chr1:84968600-84970000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:84968600-84970000	Enhancers	Fetal Intestine Large	intestine
41	chr1:84968600-84970000	Flanking Active TSS	NHLF	lung
42	chr1:84968600-84970200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:84968600-84970200	Enhancers	Fetal Muscle Leg	muscle
44	chr1:84968600-84970600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:84968600-84970600	Enhancers	Stomach Mucosa	stomach
46	chr1:84968600-84970800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:84968600-84971400	Active TSS	Right Atrium	heart
48	chr1:84968800-84969600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:84968800-84969800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:84968800-84969800	Enhancers	Fetal Kidney	kidney

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