Variant report

Variant	rs2000175
Chromosome Location	chr10:6315852-6315853
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	chr10:6315737-6315885	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6298094..6299703-chr10:6315847..6318210,2	K562	blood:
2	chr10:6282149..6284727-chr10:6315762..6318324,2	MCF-7	breast:
3	chr10:6263461..6265424-chr10:6315540..6318347,2	K562	blood:
4	chr10:6315744..6318557-chr10:6324362..6327145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215244	TF binding region
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2000173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2387150	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4347290	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7077335	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6309600-6317000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:6309600-6317000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:6309600-6317200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:6312800-6316000	Enhancers	Liver	Liver
5	chr10:6312800-6316400	Weak transcription	Primary B cells from cord blood	blood
6	chr10:6312800-6316600	Weak transcription	NHEK	skin
7	chr10:6312800-6316800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:6312800-6317000	Weak transcription	Spleen	Spleen
9	chr10:6313200-6316400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr10:6313200-6316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:6313200-6316800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:6313200-6316800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:6313400-6316400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:6313400-6316400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:6313400-6316600	Weak transcription	Small Intestine	intestine
16	chr10:6313400-6316800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:6313400-6317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:6313400-6317200	Weak transcription	Fetal Intestine Small	intestine
19	chr10:6313400-6317200	Weak transcription	Thymus	Thymus
20	chr10:6313600-6316800	Weak transcription	HSMMtube	muscle
21	chr10:6313600-6317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr10:6313600-6317000	Weak transcription	Fetal Thymus	thymus
23	chr10:6313800-6316800	Weak transcription	Brain Anterior Caudate	brain
24	chr10:6313800-6317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:6313800-6317000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr10:6313800-6317000	Weak transcription	Primary T cells from cord blood	blood
27	chr10:6313800-6317000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:6313800-6317000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr10:6313800-6321000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:6314000-6316600	Weak transcription	HMEC	breast
31	chr10:6314000-6316800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:6314200-6316600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr10:6314200-6316800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:6314200-6316800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:6314200-6316800	Weak transcription	GM12878-XiMat	blood
36	chr10:6314200-6317000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr10:6314200-6317000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr10:6314200-6317000	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:6314200-6317000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:6314200-6317000	Weak transcription	Esophagus	oesophagus
41	chr10:6314200-6317000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:6314200-6317000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:6314200-6317000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr10:6314400-6316600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:6314400-6316600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:6314400-6316800	Weak transcription	Brain Substantia Nigra	brain
47	chr10:6314400-6316800	Weak transcription	Stomach Mucosa	stomach
48	chr10:6314400-6317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:6314400-6317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:6314400-6317000	Weak transcription	Brain Inferior Temporal Lobe	brain

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