Variant report

Variant	rs10460482
Chromosome Location	chr2:98644179-98644180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98612077..98616109-chr2:98644119..98647261,6	MCF-7	breast:
2	chr2:98643410..98646144-chr2:98647882..98649628,2	K562	blood:
3	chr2:98610702..98614249-chr2:98641205..98645622,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12617912	0.91[ASN][1000 genomes]
rs1668781	0.83[ASN][1000 genomes]
rs1995455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56266798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60907581	0.85[ASN][1000 genomes]
rs61485686	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73960446	0.91[ASN][1000 genomes]
rs7587637	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv834309	chr2:98643304-98793838	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10460482	HERC2P4	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98638000-98644800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:98638000-98656600	Weak transcription	Right Atrium	heart
3	chr2:98638400-98644600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:98642400-98644200	Enhancers	Primary T cells from cord blood	blood
5	chr2:98642400-98644800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr2:98642600-98644400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:98642600-98644400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:98642600-98644400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:98642600-98644600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:98642600-98644600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:98642600-98644800	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:98642600-98645000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr2:98642600-98645000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:98642800-98644400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:98642800-98644600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:98642800-98644600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:98642800-98644600	Enhancers	Fetal Thymus	thymus
18	chr2:98642800-98645000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:98642800-98646600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:98643000-98644400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:98643000-98644600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:98643000-98646800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:98643200-98644200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:98643200-98644600	Enhancers	Brain Hippocampus Middle	brain
25	chr2:98643200-98644600	Enhancers	Psoas Muscle	Psoas
26	chr2:98643200-98644600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:98643200-98646200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:98643200-98647600	Enhancers	Stomach Mucosa	stomach
29	chr2:98643200-98650200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:98643400-98644400	Enhancers	Fetal Muscle Leg	muscle
31	chr2:98643400-98644800	Enhancers	Brain Anterior Caudate	brain
32	chr2:98643600-98644200	Weak transcription	Spleen	Spleen
33	chr2:98643600-98644400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:98643600-98645200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:98643600-98645400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:98643600-98645600	Weak transcription	Colonic Mucosa	Colon
37	chr2:98643800-98644200	Enhancers	Primary B cells from peripheral blood	blood
38	chr2:98643800-98644400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:98643800-98644600	Enhancers	Dnd41	blood
40	chr2:98643800-98645000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr2:98643800-98645200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:98643800-98645600	Weak transcription	Left Ventricle	heart
43	chr2:98643800-98646200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:98644000-98644400	Enhancers	Gastric	stomach
45	chr2:98644000-98644800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr2:98644000-98645000	Flanking Active TSS	GM12878-XiMat	blood
47	chr2:98644000-98645400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:98644000-98645800	Enhancers	Placenta	Placenta
49	chr2:98644000-98646800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:98644000-98646800	Enhancers	Osteobl	bone

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