Variant report

Variant	rs2254974
Chromosome Location	chr6:25336402-25336403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25331246..25333492-chr6:25335317..25337907,2	K562	blood:
2	chr6:25278190..25281411-chr6:25333036..25336793,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2690059	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs2744234	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2744237	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[AFR][1000 genomes]
rs6456678	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];0.86[AFR][1000 genomes]
rs6933921	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs760864	0.84[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2254974	HIST1H2BE	cis	parietal	SCAN
rs2254974	HIST1H2AE	cis	cerebellum	SCAN
rs2254974	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:25327600-25337400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:25328200-25336800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:25328200-25338200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:25330400-25337200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:25331200-25336800	Enhancers	Right Atrium	heart
7	chr6:25331400-25336600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:25332000-25336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:25332000-25336600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:25332000-25337200	Weak transcription	Fetal Brain Female	brain
12	chr6:25332000-25337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:25332000-25337800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:25332000-25346800	Weak transcription	Ovary	ovary
18	chr6:25332200-25337600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:25332600-25336800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:25332600-25339800	Weak transcription	Colonic Mucosa	Colon
21	chr6:25332800-25337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:25332800-25341200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
24	chr6:25333400-25337600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:25333400-25340800	Weak transcription	Aorta	Aorta
26	chr6:25333800-25336600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:25333800-25337000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:25333800-25346400	Weak transcription	Left Ventricle	heart
29	chr6:25334200-25341200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:25334400-25339400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:25334400-25342000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:25334600-25337400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:25334800-25336600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr6:25335000-25337200	Enhancers	Fetal Intestine Large	intestine
35	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
36	chr6:25335400-25336600	Weak transcription	Fetal Kidney	kidney
37	chr6:25335400-25337000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:25335400-25337600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:25335400-25342600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:25335600-25336600	Weak transcription	Fetal Lung	lung
41	chr6:25335600-25337400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:25335600-25337400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:25335600-25339800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:25335600-25340800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:25335600-25340800	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:25336000-25336600	Weak transcription	Esophagus	oesophagus
47	chr6:25336000-25336800	Enhancers	Small Intestine	intestine
48	chr6:25336000-25337400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:25336000-25337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:25336200-25336800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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