Variant report

Variant	rs2002322
Chromosome Location	chr19:52776670-52776671
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52775386..52777068-chr19:52798761..52801012,2	MCF-7	breast:
2	chr19:52764752..52766794-chr19:52774661..52777312,2	K562	blood:
3	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
4	chr19:52774375..52777116-chr19:52786827..52789950,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10520481	1.00[JPT][hapmap]
rs13344871	1.00[JPT][hapmap]
rs16983537	1.00[JPT][hapmap]
rs16983625	1.00[JPT][hapmap]
rs16983630	1.00[JPT][hapmap]
rs2002323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560903	1.00[JPT][hapmap]
rs2657925	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2657932	1.00[JPT][hapmap]
rs7251497	1.00[JPT][hapmap]
rs7251605	1.00[JPT][hapmap]
rs8107383	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52776800	Weak transcription	Psoas Muscle	Psoas
2	chr19:52774000-52780000	Weak transcription	Aorta	Aorta
3	chr19:52774000-52780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
5	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:52774200-52777400	Weak transcription	HSMMtube	muscle
7	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
10	chr19:52774400-52777000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:52774400-52777200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:52774400-52777200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:52774400-52777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:52774400-52777800	ZNF genes & repeats	A549	lung
15	chr19:52774400-52778400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:52774400-52778400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
17	chr19:52774400-52779200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:52774400-52781000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:52774400-52782000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:52774400-52786600	Weak transcription	Osteobl	bone
21	chr19:52774400-52787000	Weak transcription	HUVEC	blood vessel
22	chr19:52774400-52787400	Weak transcription	NHDF-Ad	bronchial
23	chr19:52774600-52777000	Weak transcription	Stomach Mucosa	stomach
24	chr19:52774600-52777200	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr19:52774600-52777200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:52774600-52777200	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr19:52774600-52777200	Weak transcription	Fetal Kidney	kidney
28	chr19:52774600-52777400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr19:52774600-52777600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:52774600-52777800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr19:52774600-52777800	ZNF genes & repeats	Fetal Thymus	thymus
32	chr19:52774600-52778600	ZNF genes & repeats	Thymus	Thymus
33	chr19:52774600-52780000	Weak transcription	Colonic Mucosa	Colon
34	chr19:52774600-52780400	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr19:52774600-52781200	ZNF genes & repeats	GM12878-XiMat	blood
36	chr19:52774600-52782000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:52774600-52782600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr19:52774600-52783600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:52774600-52783800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr19:52774600-52786400	Weak transcription	Brain Angular Gyrus	brain
41	chr19:52774600-52786600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr19:52774800-52776800	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:52774800-52776800	Weak transcription	Fetal Brain Male	brain
45	chr19:52774800-52776800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr19:52774800-52777000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:52774800-52777600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:52774800-52777800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr19:52774800-52777800	Genic enhancers	Dnd41	blood
50	chr19:52774800-52778000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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