Variant report

Variant	rs10197101
Chromosome Location	chr2:39972302-39972303
allele	C/T
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	chr2:39969387-39972759	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39971834..39974291-chr2:39976414..39978177,2	K562	blood:

Variant related genes	Relation type
THUMPD2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10168666	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10171615	1.00[AMR][1000 genomes]
rs10177342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12712654	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs12712655	0.94[AFR][1000 genomes]
rs13393172	0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs13412186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416764	1.00[AMR][1000 genomes]
rs17024276	0.83[AFR][1000 genomes]
rs59146573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61706206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544243	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs6725034	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742533	0.94[YRI][hapmap]
rs6744797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749057	0.94[YRI][hapmap];0.97[AFR][1000 genomes]
rs6761738	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924903	1.00[AMR][1000 genomes]
rs7564579	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603886	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
2	chr2:39959400-39974200	Strong transcription	Primary B cells from cord blood	blood
3	chr2:39960200-39973800	Strong transcription	Primary hematopoietic stem cells	blood
4	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:39960400-39973600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
7	chr2:39961200-39974600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
9	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:39962200-39993200	Strong transcription	Liver	Liver
11	chr2:39962800-39980200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:39963200-39982000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:39964000-39976800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:39964200-39976800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:39964200-39977000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:39964200-39977400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
18	chr2:39964400-39977000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:39964800-39983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:39965200-39976600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:39965200-39980000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:39965200-39983000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:39965400-39972400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:39965400-39984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:39965600-39975400	Weak transcription	Fetal Kidney	kidney
28	chr2:39965800-39972600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:39966000-39973000	Weak transcription	Fetal Intestine Small	intestine
30	chr2:39966600-39976800	Weak transcription	Small Intestine	intestine
31	chr2:39966800-39975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:39966800-39980000	Weak transcription	Esophagus	oesophagus
33	chr2:39966800-39980200	Weak transcription	Lung	lung
34	chr2:39966800-39983200	Weak transcription	Spleen	Spleen
35	chr2:39967000-39973000	Weak transcription	Pancreas	Pancrea
36	chr2:39967000-39976200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:39967000-39976800	Weak transcription	Gastric	stomach
38	chr2:39967000-39981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:39967000-39983000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:39967000-39983200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39967000-39983400	Weak transcription	Aorta	Aorta
42	chr2:39967200-39976600	Weak transcription	Brain Germinal Matrix	brain
43	chr2:39967200-39983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:39967600-39976800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:39967800-39976400	Weak transcription	Brain Anterior Caudate	brain
47	chr2:39968200-39973000	Weak transcription	Fetal Stomach	stomach
48	chr2:39969400-39974000	Strong transcription	Placenta	Placenta
49	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:39970000-39972800	Strong transcription	Hela-S3	cervix

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