Variant report

Variant	rs1984298
Chromosome Location	chr1:78296282-78296283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78291093..78292647-chr1:78295920..78298177,2	MCF-7	breast:
2	chr1:78294723..78298256-chr1:78467629..78470494,3	K562	blood:
3	chr1:78296217..78298121-chr1:78469672..78471231,2	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12404652	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs12409081	1.00[ASN][1000 genomes]
rs1749912	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4245659	1.00[YRI][hapmap]
rs6424666	1.00[ASN][1000 genomes]
rs6656888	0.82[MEX][hapmap]
rs6704477	1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7531525	1.00[ASN][1000 genomes]
rs9662911	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
2	chr1:78266000-78298000	Weak transcription	K562	blood
3	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
5	chr1:78274800-78297400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:78274800-78297600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:78274800-78298000	Weak transcription	Fetal Kidney	kidney
8	chr1:78275000-78312800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:78279200-78300400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:78280400-78297400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:78280600-78298000	Weak transcription	Fetal Brain Male	brain
12	chr1:78280600-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:78281000-78296600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:78281000-78308800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:78281200-78316400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:78281600-78297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:78283200-78296600	Weak transcription	Right Ventricle	heart
19	chr1:78284400-78297400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:78284400-78303200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:78284600-78333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:78284800-78297800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:78285000-78310200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:78285600-78332000	Weak transcription	Spleen	Spleen
25	chr1:78285800-78298000	Weak transcription	Brain Anterior Caudate	brain
26	chr1:78285800-78308800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:78286400-78296400	Weak transcription	Primary T cells from cord blood	blood
28	chr1:78286400-78298000	Weak transcription	GM12878-XiMat	blood
29	chr1:78286400-78298200	Weak transcription	Colonic Mucosa	Colon
30	chr1:78286400-78333200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:78286600-78312800	Weak transcription	Thymus	Thymus
32	chr1:78286600-78328400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:78287400-78310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:78288000-78298000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:78288200-78298000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:78288200-78299400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:78288200-78309000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:78289400-78298000	Weak transcription	Fetal Brain Female	brain
39	chr1:78290000-78296600	Weak transcription	Primary B cells from cord blood	blood
40	chr1:78290000-78298000	Weak transcription	A549	lung
41	chr1:78290200-78296400	Weak transcription	Fetal Lung	lung
42	chr1:78290200-78297800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:78290200-78300000	Weak transcription	Fetal Intestine Large	intestine
44	chr1:78290200-78334200	Weak transcription	Gastric	stomach
45	chr1:78290600-78297400	Weak transcription	Adipose Nuclei	Adipose
46	chr1:78290800-78297400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:78291000-78296400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:78291000-78298200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:78291000-78299800	Weak transcription	Placenta	Placenta
50	chr1:78291400-78296400	Weak transcription	Stomach Smooth Muscle	stomach

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