Variant report

Variant	rs3112149
Chromosome Location	chr2:39055118-39055119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
2	chr2:38976908..38981867-chr2:39050395..39056507,16	K562	blood:
3	chr2:38970642..38974334-chr2:39052366..39056279,4	K562	blood:
4	chr2:38974988..38979943-chr2:39053736..39058253,10	K562	blood:
5	chr2:39053934..39056407-chr2:39351577..39353846,2	K562	blood:
6	chr2:39053503..39055563-chr2:39060007..39062643,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10168789	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10173118	0.85[ASN][1000 genomes]
rs10173240	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10176932	0.81[ASN][1000 genomes]
rs10865144	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694383	0.81[EUR][1000 genomes]
rs11889280	0.80[EUR][1000 genomes]
rs12465043	0.86[ASN][1000 genomes]
rs12465365	0.82[ASN][1000 genomes]
rs12468732	0.80[ASN][1000 genomes]
rs12469681	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12473036	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12477252	0.85[ASN][1000 genomes]
rs12623330	0.82[ASN][1000 genomes]
rs12712621	0.90[ASN][1000 genomes]
rs12712622	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712624	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12996194	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011522	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13014136	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13029406	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13383541	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13411868	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13417196	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530852	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530853	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1979142	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099965	0.83[EUR][1000 genomes]
rs3099984	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099988	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099989	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099991	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112140	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112205	0.82[EUR][1000 genomes]
rs3112210	0.85[EUR][1000 genomes]
rs3112216	0.82[EUR][1000 genomes]
rs3770681	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670894	0.83[ASN][1000 genomes]
rs4670897	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56393601	0.81[EUR][1000 genomes]
rs60012208	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723868	0.95[ASN][1000 genomes]
rs6753251	0.80[EUR][1000 genomes]
rs7419616	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7589162	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591959	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7602287	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3112149	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
4	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
6	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:39038800-39102200	Weak transcription	Gastric	stomach
11	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
13	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
15	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
19	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
20	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
22	chr2:39046200-39070200	Weak transcription	NHLF	lung
23	chr2:39046400-39057200	Weak transcription	HepG2	liver
24	chr2:39048000-39055600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
26	chr2:39049000-39056000	Strong transcription	Fetal Intestine Small	intestine
27	chr2:39049400-39055400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:39049600-39055600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:39049600-39055600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:39049600-39056200	Strong transcription	Fetal Intestine Large	intestine
31	chr2:39049800-39056000	Strong transcription	Brain Germinal Matrix	brain
32	chr2:39050000-39055600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:39050000-39055600	Strong transcription	Dnd41	blood
34	chr2:39050400-39062800	Weak transcription	Thymus	Thymus
35	chr2:39050400-39063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
39	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:39051000-39068600	Weak transcription	HMEC	breast
41	chr2:39052000-39061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:39052200-39068600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:39053000-39057200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:39053200-39068600	Weak transcription	Brain Substantia Nigra	brain
45	chr2:39053200-39069600	Weak transcription	HUVEC	blood vessel
46	chr2:39053600-39057400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:39053600-39060000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:39053600-39062400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:39053800-39055600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:39053800-39057200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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