Variant report

Variant	rs3112992
Chromosome Location	chr2:95784975-95784976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95784064..95788692-chr2:95827645..95832682,10	MCF-7	breast:
2	chr2:95783537..95785455-chr2:95785676..95787483,2	K562	blood:
3	chr2:95784181..95785707-chr2:95832931..95835537,2	K562	blood:
4	chr2:95741563..95744104-chr2:95781208..95785106,3	MCF-7	breast:
5	chr2:95784318..95786550-chr2:95817461..95819356,2	K562	blood:
6	chr2:95784303..95789114-chr2:95829766..95832778,9	MCF-7	breast:
7	chr2:95782670..95785477-chr2:95785880..95788763,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144026	Chromatin interaction
ENSG00000163067	Chromatin interaction
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs3112226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112989	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3112994	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112998	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6719142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs889854	0.89[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[YRI][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	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3112992	SRA1	trans	parietal	SCAN
rs3112992	ACTR1B	cis	cerebellum	SCAN
rs3112992	ZNF514	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95764000-95786200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:95774200-95786800	Weak transcription	Aorta	Aorta
3	chr2:95774600-95785400	Weak transcription	Esophagus	oesophagus
4	chr2:95774800-95786200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:95775400-95786000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:95775600-95785000	Weak transcription	Fetal Heart	heart
7	chr2:95776000-95785400	Weak transcription	Fetal Brain Male	brain
8	chr2:95776000-95785600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:95776400-95785000	Weak transcription	Psoas Muscle	Psoas
10	chr2:95777200-95785800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:95778600-95786000	Weak transcription	NHLF	lung
12	chr2:95779600-95786600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:95779800-95785600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:95779800-95786200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:95780000-95785400	Weak transcription	Small Intestine	intestine
16	chr2:95780000-95785600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:95780000-95786400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:95780200-95785000	Weak transcription	Colonic Mucosa	Colon
19	chr2:95780800-95785400	Weak transcription	Brain Angular Gyrus	brain
20	chr2:95781000-95785000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:95781000-95785000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:95781000-95785000	Weak transcription	Left Ventricle	heart
23	chr2:95781000-95785400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:95781000-95785600	Weak transcription	NHEK	skin
25	chr2:95781000-95785800	Weak transcription	HMEC	breast
26	chr2:95781000-95785800	Weak transcription	NHDF-Ad	bronchial
27	chr2:95781000-95786000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:95781000-95786000	Weak transcription	NH-A	brain
29	chr2:95781000-95786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:95781000-95786200	Weak transcription	HSMMtube	muscle
31	chr2:95781000-95786400	Weak transcription	Fetal Intestine Large	intestine
32	chr2:95781000-95786400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:95781000-95787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:95781200-95785600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:95781200-95785600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:95781200-95785600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:95781200-95785600	Weak transcription	Placenta	Placenta
38	chr2:95781400-95785000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:95781400-95785200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:95781400-95785200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:95781400-95785200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:95781400-95785600	Weak transcription	Brain Anterior Caudate	brain
43	chr2:95781400-95785600	Weak transcription	Fetal Lung	lung
44	chr2:95781400-95785600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:95781400-95785600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:95781400-95785800	Weak transcription	Stomach Mucosa	stomach
47	chr2:95781400-95786000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:95781400-95786000	Weak transcription	HSMM	muscle
49	chr2:95781400-95786000	Weak transcription	Osteobl	bone
50	chr2:95781600-95785000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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