Variant report

Variant	rs7641299
Chromosome Location	chr3:100170553-100170554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10936193	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1144126	0.85[YRI][hapmap]
rs1145348	0.85[YRI][hapmap]
rs11707581	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12591	0.92[CEU][hapmap]
rs1718272	0.85[YRI][hapmap]
rs17279967	0.86[JPT][hapmap];0.84[TSI][hapmap]
rs2068018	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs2289501	0.80[CEU][hapmap]
rs58079517	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586347	0.85[YRI][hapmap]
rs610854	0.85[YRI][hapmap]
rs73150369	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7641299	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs7641299	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs7641299	NIT2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100144200-100175600	Weak transcription	Psoas Muscle	Psoas
2	chr3:100146400-100177800	Weak transcription	Ovary	ovary
3	chr3:100148200-100182400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:100149400-100171800	Weak transcription	Aorta	Aorta
5	chr3:100158400-100176400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:100163000-100177200	Weak transcription	HepG2	liver
7	chr3:100163400-100176400	Weak transcription	Fetal Lung	lung
8	chr3:100166800-100173600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:100167600-100170800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:100167600-100171000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:100168000-100171200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:100168400-100170600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:100168600-100176200	Weak transcription	Brain Angular Gyrus	brain
14	chr3:100168800-100171600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:100168800-100174000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:100168800-100175600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:100168800-100177800	Weak transcription	Left Ventricle	heart
18	chr3:100169000-100170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:100169000-100171800	Weak transcription	Liver	Liver
20	chr3:100169200-100171200	Weak transcription	Fetal Stomach	stomach
21	chr3:100169400-100170600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:100169400-100170800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:100169400-100175600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:100169600-100171200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:100169800-100174400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:100169800-100176400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:100170000-100172600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:100170000-100172800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:100170000-100174600	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:100170200-100170800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:100170200-100175000	Weak transcription	Fetal Brain Female	brain
32	chr3:100170400-100170800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:100170400-100170800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:100170400-100173000	Weak transcription	Fetal Intestine Small	intestine

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