Variant report

Variant	rs6544054
Chromosome Location	chr2:37338314-37338315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37336683..37339266-chr2:37345698..37347982,2	K562	blood:
2	chr2:37331802..37334413-chr2:37337441..37339109,2	K562	blood:
3	chr2:37311072..37312864-chr2:37336660..37338534,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152133	Chromatin interaction
ENSG00000008869	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10177315	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194972	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11892108	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11892180	1.00[ASN][1000 genomes]
rs11894496	1.00[ASN][1000 genomes]
rs13388882	1.00[ASN][1000 genomes]
rs13414561	1.00[CHB][hapmap]
rs13425846	1.00[ASN][1000 genomes]
rs13429945	1.00[CHB][hapmap]
rs2307472	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2307474	1.00[ASN][1000 genomes]
rs2307483	1.00[CHB][hapmap]
rs2372443	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373114	1.00[CHB][hapmap]
rs2373188	1.00[ASN][1000 genomes]
rs3856498	1.00[ASN][1000 genomes]
rs4233920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648150	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648153	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648158	1.00[ASN][1000 genomes]
rs4648160	1.00[ASN][1000 genomes]
rs4648166	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648169	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648170	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648171	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648190	1.00[ASN][1000 genomes]
rs4648191	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648196	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648199	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4648202	1.00[CHB][hapmap]
rs4648212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648216	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648218	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55679447	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55939105	1.00[ASN][1000 genomes]
rs62621388	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544053	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6544055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544056	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720519	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726403	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726768	1.00[CHB][hapmap]
rs6726921	1.00[CHB][hapmap]
rs6733861	1.00[CHB][hapmap]
rs6734153	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6735749	1.00[AFR][1000 genomes]
rs6738111	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6740307	1.00[ASN][1000 genomes]
rs6749793	1.00[CHB][hapmap]
rs6754376	1.00[CHB][hapmap]
rs6758981	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7568925	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590377	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759668	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs759669	1.00[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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised 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	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544054	CCDC75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37312200-37346000	Weak transcription	Pancreas	Pancrea
2	chr2:37312200-37383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:37313200-37346000	Weak transcription	Stomach Mucosa	stomach
4	chr2:37313400-37361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:37314400-37347000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:37314600-37346800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:37315600-37367000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:37315800-37341200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:37315800-37341400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:37319000-37341200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:37319000-37346600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:37319000-37347000	Strong transcription	Dnd41	blood
13	chr2:37319200-37377200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:37320000-37346600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:37320600-37368000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:37321600-37344800	Weak transcription	Gastric	stomach
17	chr2:37321600-37348600	Weak transcription	Colonic Mucosa	Colon
18	chr2:37322400-37352200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:37323400-37340600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:37324800-37344400	Strong transcription	Adipose Nuclei	Adipose
21	chr2:37326800-37346600	Strong transcription	GM12878-XiMat	blood
22	chr2:37327000-37349200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:37328000-37339200	Weak transcription	Esophagus	oesophagus
24	chr2:37328200-37349000	Weak transcription	Aorta	Aorta
25	chr2:37329400-37345600	Weak transcription	NHLF	lung
26	chr2:37330400-37339600	Strong transcription	Fetal Intestine Small	intestine
27	chr2:37330600-37340400	Strong transcription	Fetal Intestine Large	intestine
28	chr2:37330800-37338400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:37330800-37339600	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:37330800-37340600	Strong transcription	Fetal Thymus	thymus
31	chr2:37331000-37341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:37331200-37348800	Weak transcription	K562	blood
33	chr2:37331400-37338600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:37331400-37346800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:37331600-37339600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:37331600-37347200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:37331600-37347400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:37332400-37338400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:37332400-37341200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:37332400-37344000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:37332600-37338400	Strong transcription	Fetal Brain Female	brain
42	chr2:37332600-37340200	Strong transcription	A549	lung
43	chr2:37332600-37340400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:37332600-37346600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:37332600-37375200	Strong transcription	Liver	Liver
46	chr2:37332800-37346600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:37332800-37351200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:37333000-37340400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:37333200-37339600	Strong transcription	Fetal Lung	lung
50	chr2:37333200-37341200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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