Variant report

Variant	rs10202174
Chromosome Location	chr2:30704023-30704024
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30702205..30704155-chr2:30801614..30803584,2	K562	blood:
2	chr2:30703972..30706142-chr2:30708659..30711183,2	MCF-7	breast:
3	chr2:30699042..30701340-chr2:30702714..30704387,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10180482	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10201729	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12053230	0.81[ASN][1000 genomes]
rs12993078	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13014119	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017224	0.94[ASN][1000 genomes]
rs13025287	0.82[ASN][1000 genomes]
rs13395754	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357850	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525063	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17038632	0.84[ASN][1000 genomes]
rs2076932	0.82[EUR][1000 genomes]
rs28666424	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35116667	0.98[ASN][1000 genomes]
rs36072623	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56150357	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62139608	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705814	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6724421	0.94[EUR][1000 genomes]
rs6739322	0.84[ASN][1000 genomes]
rs894788	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10202174	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs10202174	LYCAT	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
3	chr2:30678600-30710600	Weak transcription	NHLF	lung
4	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:30688400-30704200	Weak transcription	Aorta	Aorta
6	chr2:30688400-30704600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:30695200-30707000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:30695400-30704400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:30695600-30704200	Weak transcription	Fetal Lung	lung
11	chr2:30695600-30705400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:30695800-30704400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:30696000-30704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:30696200-30710600	Weak transcription	Ovary	ovary
16	chr2:30697200-30704200	Weak transcription	Fetal Intestine Large	intestine
17	chr2:30697400-30710400	Weak transcription	Fetal Kidney	kidney
18	chr2:30697800-30704200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
20	chr2:30698000-30708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:30698000-30709400	Weak transcription	Pancreas	Pancrea
22	chr2:30698200-30704200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:30698200-30704200	Weak transcription	Right Atrium	heart
24	chr2:30698200-30704400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:30698400-30706800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:30698600-30704400	Weak transcription	Primary B cells from cord blood	blood
28	chr2:30699000-30709600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:30699600-30709400	Weak transcription	Right Ventricle	heart
31	chr2:30699800-30704200	Weak transcription	Psoas Muscle	Psoas
32	chr2:30701200-30704400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:30701200-30705600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:30701200-30714400	Weak transcription	HSMM	muscle
35	chr2:30701400-30704200	Weak transcription	Esophagus	oesophagus
36	chr2:30701600-30704200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:30702200-30704200	Weak transcription	Fetal Thymus	thymus
38	chr2:30702200-30704400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:30702800-30704200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:30702800-30710400	Weak transcription	Primary T cells from cord blood	blood
41	chr2:30703400-30704200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:30703400-30704400	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:30703400-30704600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:30703400-30704600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr2:30703400-30704800	Enhancers	K562	blood
46	chr2:30703600-30704200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:30703600-30704200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:30703600-30704600	Enhancers	Fetal Intestine Small	intestine
49	chr2:30703600-30704800	Enhancers	Stomach Mucosa	stomach
50	chr2:30703600-30705000	Enhancers	GM12878-XiMat	blood

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