Variant report

Variant	rs2857861
Chromosome Location	chr4:3323767-3323768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3321816..3324737-chr4:3338680..3341161,2	MCF-7	breast:
2	chr4:3316926..3319273-chr4:3321348..3323892,2	K562	blood:
3	chr4:3312683..3315321-chr4:3322350..3324047,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248840	Chromatin interaction
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2051558	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071666	0.88[EUR][1000 genomes]
rs2749781	0.81[JPT][hapmap]
rs2749782	0.80[MEX][hapmap]
rs2749783	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2749785	0.85[CHB][hapmap]
rs3129308	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3129310	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs3129314	0.88[EUR][1000 genomes]
rs3129316	0.83[EUR][1000 genomes]
rs3129328	0.86[CHB][hapmap]
rs6446731	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs881817	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
11	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2857861	HGFAC	cis	cerebellum	SCAN
rs2857861	EVC	cis	cerebellum	SCAN
rs2857861	RGS12	cis	cerebellum	SCAN
rs2857861	ATP5I	cis	parietal	SCAN
rs2857861	DOK7	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3307200-3327000	Weak transcription	Fetal Kidney	kidney
3	chr4:3307400-3325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:3307400-3326800	Weak transcription	A549	lung
5	chr4:3308000-3323800	Weak transcription	Osteobl	bone
6	chr4:3308000-3326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:3308000-3327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:3309000-3327200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:3314200-3326600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:3314400-3327400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:3314400-3328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:3315400-3326600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:3319200-3332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:3319600-3323800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:3319800-3332000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr4:3320000-3344000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:3320200-3324000	Genic enhancers	Fetal Intestine Small	intestine
19	chr4:3320200-3328400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:3320400-3326400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:3320400-3326400	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:3320400-3327400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
24	chr4:3320600-3323800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:3320600-3332200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:3320800-3327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:3321000-3323800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:3321000-3324600	Enhancers	Fetal Heart	heart
29	chr4:3321000-3325800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:3321000-3326000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:3321000-3347000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:3321400-3324200	Enhancers	Left Ventricle	heart
33	chr4:3321400-3324200	Enhancers	Right Ventricle	heart
34	chr4:3321600-3324000	Enhancers	Psoas Muscle	Psoas
35	chr4:3321600-3324200	Enhancers	Fetal Muscle Leg	muscle
36	chr4:3321600-3324600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:3321600-3326000	Enhancers	Fetal Brain Male	brain
38	chr4:3321800-3324000	Enhancers	Lung	lung
39	chr4:3322000-3324000	Enhancers	Right Atrium	heart
40	chr4:3322000-3326000	Enhancers	HUVEC	blood vessel
41	chr4:3322000-3326400	Enhancers	HepG2	liver
42	chr4:3322200-3324000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr4:3322200-3324000	Genic enhancers	Fetal Stomach	stomach
44	chr4:3322200-3324200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:3322200-3324200	Enhancers	Stomach Mucosa	stomach
46	chr4:3322200-3324800	Enhancers	Brain Anterior Caudate	brain
47	chr4:3322200-3325200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:3322400-3323800	Enhancers	Fetal Brain Female	brain
49	chr4:3322400-3324000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:3322400-3324000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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