Variant report

Variant	rs3804538
Chromosome Location	chr6:143778954-143778955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143777826..143779334-chr6:143832308..143834105,2	MCF-7	breast:
2	chr6:143769577..143772365-chr6:143778792..143780914,2	MCF-7	breast:
3	chr6:143771894..143773645-chr6:143774533..143780874,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223203	Chromatin interaction
ENSG00000034693	Chromatin interaction
ENSG00000001036	Chromatin interaction
ENSG00000189007	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1061220	0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs1065355	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10782288	0.91[EUR][1000 genomes]
rs10782289	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10809	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12196227	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12199192	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338533	0.88[EUR][1000 genomes]
rs1424922	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1978529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143137	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2272924	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs2294505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294506	1.00[CEU][hapmap];0.97[TSI][hapmap]
rs2496593	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3088203	0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs3761999	0.81[JPT][hapmap]
rs3762000	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs3762001	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3762002	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3789789	0.84[EUR][1000 genomes]
rs3789790	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3789791	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804544	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895612	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4895614	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4895615	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4896656	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4896659	0.90[EUR][1000 genomes]
rs4896660	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6924268	0.91[EUR][1000 genomes]
rs6926733	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6929191	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6930325	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6935346	1.00[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs6935618	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs7741976	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7751011	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321913	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321914	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9373391	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9373393	1.00[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9376750	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376753	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9390092	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs9390094	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390096	0.94[CEU][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs9399442	0.92[EUR][1000 genomes]
rs9399443	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403492	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403494	0.85[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403496	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3804538	RAB32	cis	parietal	SCAN
rs3804538	FUCA2	cis	parietal	SCAN
rs3804538	HIVEP2	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143772600-143780600	Weak transcription	Left Ventricle	heart
2	chr6:143772600-143780800	Weak transcription	Esophagus	oesophagus
3	chr6:143772600-143790000	Weak transcription	Pancreas	Pancrea
4	chr6:143772600-143790000	Weak transcription	Spleen	Spleen
5	chr6:143772600-143791200	Weak transcription	Lung	lung
6	chr6:143772600-143811600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:143772600-143832000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:143772800-143780600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:143772800-143780600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:143772800-143780600	Weak transcription	Placenta	Placenta
11	chr6:143772800-143780800	Weak transcription	Fetal Thymus	thymus
12	chr6:143772800-143784000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:143772800-143796600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:143772800-143798600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:143772800-143815000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:143772800-143821200	Weak transcription	Psoas Muscle	Psoas
17	chr6:143773000-143780400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:143773000-143780600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:143773000-143780600	Weak transcription	Fetal Intestine Large	intestine
20	chr6:143773000-143780600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:143773000-143781800	Weak transcription	Fetal Stomach	stomach
22	chr6:143773000-143782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:143773000-143782000	Weak transcription	Ovary	ovary
24	chr6:143773000-143784000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:143773000-143791400	Weak transcription	Thymus	Thymus
26	chr6:143773000-143793400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:143773000-143793600	Weak transcription	HSMMtube	muscle
28	chr6:143773000-143797400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:143773000-143801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:143773000-143811600	Weak transcription	Right Ventricle	heart
31	chr6:143773000-143814600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:143773000-143814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:143773000-143815000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:143773000-143815000	Weak transcription	Colonic Mucosa	Colon
35	chr6:143773200-143780200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:143773200-143780600	Weak transcription	Adipose Nuclei	Adipose
37	chr6:143773200-143793000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:143773200-143793000	Weak transcription	Brain Substantia Nigra	brain
39	chr6:143773200-143793600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:143773200-143827000	Weak transcription	Brain Germinal Matrix	brain
41	chr6:143773400-143780200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:143773400-143780200	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:143773400-143780400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:143773400-143780600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:143773400-143780600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:143773400-143780600	Weak transcription	Brain Anterior Caudate	brain
47	chr6:143773400-143780600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:143773400-143780600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:143773400-143781600	Weak transcription	Fetal Intestine Small	intestine
50	chr6:143773400-143782000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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