Variant report

Variant	rs1046196
Chromosome Location	chr2:190611508-190611509
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	chr2:190524634..190527563-chr2:190610048..190612845,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORMDL1-3	chr2:190611390-190612603	NONHSAT076063

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1233267	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233270	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233273	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233274	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233286	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13404927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16831960	0.87[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2544054	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256571	1.00[JPT][hapmap]
rs5742924	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742965	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742976	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742991	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742994	0.81[EUR][1000 genomes]
rs5742997	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743003	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743048	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743090	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743130	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs5743161	1.00[CEU][hapmap]
rs5743164	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5743169	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5743175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs58147864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60386871	0.82[EUR][1000 genomes]
rs6750293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73042330	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73054335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054339	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735558	0.82[EUR][1000 genomes]
rs7579156	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1046196	HBG2	trans	brain	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190540800-190611800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:190540800-190618400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:190541600-190617000	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:190550800-190617000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:190550800-190626800	Weak transcription	Right Ventricle	heart
6	chr2:190551200-190617000	Weak transcription	HSMM	muscle
7	chr2:190557400-190617000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:190563600-190611800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:190563600-190612600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:190568200-190611600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:190571600-190612400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:190575000-190615800	Weak transcription	Fetal Kidney	kidney
13	chr2:190576800-190627000	Weak transcription	Pancreas	Pancrea
14	chr2:190577000-190611600	Weak transcription	Ovary	ovary
15	chr2:190577000-190622600	Weak transcription	Aorta	Aorta
16	chr2:190577200-190611800	Weak transcription	Fetal Stomach	stomach
17	chr2:190580000-190611600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:190583000-190626800	Weak transcription	Psoas Muscle	Psoas
19	chr2:190589400-190626600	Weak transcription	HUVEC	blood vessel
20	chr2:190589600-190611600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:190590800-190614800	Weak transcription	Esophagus	oesophagus
22	chr2:190591000-190612800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:190591800-190611800	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:190593600-190611800	Weak transcription	Left Ventricle	heart
25	chr2:190594800-190627000	Weak transcription	Gastric	stomach
26	chr2:190596200-190612000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:190597800-190626600	Weak transcription	Fetal Heart	heart
28	chr2:190599000-190626800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:190600800-190616600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:190601400-190626800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:190602400-190611600	Weak transcription	Osteobl	bone
32	chr2:190602400-190617000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:190602400-190626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:190603200-190612000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:190603800-190626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:190604400-190611800	Weak transcription	Thymus	Thymus
37	chr2:190605000-190626800	Weak transcription	Fetal Brain Male	brain
38	chr2:190605400-190611800	Weak transcription	GM12878-XiMat	blood
39	chr2:190606400-190611600	Weak transcription	Fetal Brain Female	brain
40	chr2:190606400-190612600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:190606600-190613200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:190606800-190611800	Weak transcription	Brain Germinal Matrix	brain
43	chr2:190606800-190613200	Strong transcription	Primary B cells from cord blood	blood
44	chr2:190607000-190619200	Weak transcription	NHDF-Ad	bronchial
45	chr2:190607000-190626800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:190607000-190626800	Weak transcription	NH-A	brain
47	chr2:190607400-190626800	Weak transcription	HSMMtube	muscle
48	chr2:190607600-190611600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:190607800-190621000	Strong transcription	Liver	Liver
50	chr2:190607800-190622400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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