Variant report

Variant	rs2115935
Chromosome Location	chr3:141616198-141616199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141609203..141611143-chr3:141614012..141616232,3	K562	blood:
2	chr3:141456404..141459700-chr3:141613701..141617116,3	MCF-7	breast:
3	chr3:141616192..141618542-chr3:141619283..141620830,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10755098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935439	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935440	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935441	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935443	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935446	0.86[CHB][hapmap]
rs11539489	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11706195	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711748	0.88[CHB][hapmap]
rs11713023	0.88[CHB][hapmap]
rs11721024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844	0.84[ASN][1000 genomes]
rs12486398	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487977	0.82[ASN][1000 genomes]
rs12487983	0.84[ASN][1000 genomes]
rs12490893	0.84[ASN][1000 genomes]
rs12494971	0.88[CHB][hapmap]
rs12497443	0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1560411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288634	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2288635	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2288636	0.88[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2861382	0.99[ASN][1000 genomes]
rs34071952	0.82[ASN][1000 genomes]
rs36038301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804772	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs3804773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828398	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4683638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683640	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683642	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683647	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4683649	0.84[ASN][1000 genomes]
rs4683651	0.80[ASN][1000 genomes]
rs55945175	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59122181	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616903	0.97[EUR][1000 genomes];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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2115935	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
2	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:141597400-141618800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:141597400-141618800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:141597800-141617200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:141597800-141617400	Weak transcription	HSMM	muscle
9	chr3:141597800-141619000	Weak transcription	Lung	lung
10	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:141598000-141618600	Weak transcription	Fetal Intestine Large	intestine
12	chr3:141598000-141618800	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:141598000-141619200	Weak transcription	Psoas Muscle	Psoas
14	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
18	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
19	chr3:141598200-141616600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
23	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:141598400-141618200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:141598400-141622200	Weak transcription	Left Ventricle	heart
26	chr3:141598400-141623800	Weak transcription	NH-A	brain
27	chr3:141600400-141618800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:141600400-141619000	Weak transcription	Fetal Brain Female	brain
29	chr3:141600600-141619400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:141600800-141618200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:141600800-141619000	Weak transcription	Adipose Nuclei	Adipose
32	chr3:141600800-141619000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:141601200-141617200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:141602400-141619000	Weak transcription	Fetal Stomach	stomach
35	chr3:141604000-141617200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:141605200-141616600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:141605200-141627200	Weak transcription	Primary T cells from cord blood	blood
38	chr3:141605600-141618800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:141606200-141623600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:141606800-141625200	Weak transcription	HSMMtube	muscle
41	chr3:141607200-141616600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:141607200-141623800	Weak transcription	HUVEC	blood vessel
43	chr3:141607400-141616800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:141608000-141618200	Weak transcription	Thymus	Thymus
45	chr3:141608000-141618800	Weak transcription	Esophagus	oesophagus
46	chr3:141609000-141618800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:141610800-141617400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:141611200-141617200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:141611600-141616800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:141612600-141619000	Weak transcription	Rectal Mucosa Donor 31	rectum

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