Variant report

Variant	rs2038740
Chromosome Location	chr6:35114542-35114543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35114280..35114831-chr6:35146899..35147456,2	MCF-7	breast:
2	chr6:35113946..35114869-chr6:35169113..35170336,5	MCF-7	breast:
3	chr6:35107375..35109588-chr6:35112053..35114587,2	K562	blood:
4	chr6:35113907..35114851-chr6:35172520..35173065,3	K562	blood:
5	chr6:35111770..35114566-chr6:35142353..35144098,2	MCF-7	breast:
6	chr6:35112797..35115026-chr6:35176369..35178563,2	MCF-7	breast:
7	chr6:35112668..35114586-chr6:35117324..35120218,2	MCF-7	breast:
8	chr6:35113898..35114772-chr6:35207672..35209207,5	MCF-7	breast:
9	chr6:35113472..35114802-chr6:35172504..35173560,6	MCF-7	breast:
10	chr6:35113848..35114843-chr6:35208586..35209665,7	K562	blood:
11	chr6:35113776..35115211-chr6:35172026..35173456,14	MCF-7	breast:
12	chr6:35113865..35114875-chr6:35207777..35209517,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124678	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10456078	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947538	0.85[EUR][1000 genomes]
rs12191117	0.83[EUR][1000 genomes]
rs12191184	0.85[EUR][1000 genomes]
rs1408256	0.80[CEU][hapmap]
rs1535814	0.80[CEU][hapmap]
rs1880090	0.83[MEX][hapmap]
rs1886242	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886243	0.80[CEU][hapmap]
rs4711404	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457804	0.91[GIH][hapmap];0.82[MEX][hapmap];0.88[EUR][1000 genomes]
rs6457805	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904920	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923951	0.80[CEU][hapmap]
rs7764636	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348967	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348968	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357195	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368849	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394274	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2038740	CYB5A	trans	lymphoblastoid	seeQTL
rs2038740	TNFRSF21	trans	lymphoblastoid	seeQTL
rs2038740	TULP1	cis	parietal	SCAN
rs2038740	NUDT3	cis	parietal	SCAN
rs2038740	HEY1	trans	lymphoblastoid	seeQTL
rs2038740	MAPK13	cis	lymphoblastoid	seeQTL
rs2038740	TWSG1	trans	lymphoblastoid	seeQTL
rs2038740	HCK	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35108200-35114600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:35110200-35117000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:35110600-35116000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:35110600-35116000	Weak transcription	HSMMtube	muscle
5	chr6:35110800-35116000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:35111000-35115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:35111200-35115800	Weak transcription	HSMM	muscle
8	chr6:35111400-35116000	Weak transcription	A549	lung
9	chr6:35113200-35118600	Enhancers	Fetal Heart	heart
10	chr6:35113400-35115400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:35113400-35116800	Enhancers	Fetal Stomach	stomach
12	chr6:35113600-35114600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:35113600-35114800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:35113600-35115400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:35113800-35115200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:35113800-35115400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:35113800-35115800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr6:35113800-35116000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:35113800-35116000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:35113800-35116000	Enhancers	NHDF-Ad	bronchial
21	chr6:35113800-35117400	Enhancers	Osteobl	bone
22	chr6:35113800-35117600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:35113800-35117600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:35114000-35114600	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:35114000-35114800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:35114000-35114800	Enhancers	Brain Substantia Nigra	brain
27	chr6:35114000-35115000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:35114000-35115200	Enhancers	Brain Hippocampus Middle	brain
29	chr6:35114000-35115600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:35114000-35115800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr6:35114000-35116400	Enhancers	Fetal Kidney	kidney
32	chr6:35114000-35117000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:35114000-35118000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:35114200-35115000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:35114200-35115200	Enhancers	Brain Anterior Caudate	brain
36	chr6:35114200-35115400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr6:35114200-35115400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr6:35114200-35115400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
39	chr6:35114200-35115600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr6:35114200-35116200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:35114400-35114600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:35114400-35114600	Enhancers	Aorta	Aorta
43	chr6:35114400-35114600	Weak transcription	Fetal Lung	lung
44	chr6:35114400-35114800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr6:35114400-35115200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr6:35114400-35115200	Enhancers	NHLF	lung
47	chr6:35114400-35115800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:35114400-35116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:35114400-35116400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr6:35114400-35117400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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